Caveat: this is not as much a criticism of the novel itself as rather that of a too superficial interpretation of the characters as perfect good guys versus evil bad guys.
Philosophically, Roark is a mere hedonist. And he was guilty for blowing up Cortlandt. Let's see why.
A careless hedonist
You said yesterday: ‘What architect isn’t interested in housing?’ I hate the whole blasted idea of it. I think it’s a worthy undertaking-to provide a decent apartment for a man who earns fifteen dollars a week. But not at the expense of other men. Not if it raises the taxes, raises all the other rents and makes the man who earns forty live in a rat hole. That’s what’s happening in New York. Nobody can afford a modern apartment-except the very rich and the paupers. Have you seen the converted brownstones in which the average self-supporting couple has to live? Have you seen their closet kitchens and their plumbing? They’re forced to live like that-because they’re not incompetent enough. They make forty dollars a week and wouldn’t be allowed into a housing project. But they’re the ones who provide the money for the damn project. They pay the taxes. And the taxes raise their own rent. And they have to move from a converted brownstone into an unconverted one and from that into a railroad flat. I’d have no desire to penalize a man because he’s worth only fifteen dollars a week. But I’ll be damned if I can see why a man worth forty must be penalized-and penalized in favor of the one who’s less competent. Sure, there are a lot of theories on the subject and volumes of discussion. But just look at the results.
-- Ayn Rand, The Fountainhead
Now any rational person would conclude, after saying this: "this is a problem, a bad thing. I don't want no part of it, I don't want to be part of the problem, in the very least. In fact, I'd rather be part of the solution, doing the good thing: "providing a decent apartment for a man who earns fifteen dollars a week, but not at the expense of other men", and having fun doing it, and making a profit doing it. Indeed, why would I contribute to something that is inherently unjust, will not be in my long-term interest either, will in fact hurt both me and others in the long run, and do it for free, to boot?
Unless of course... you only care about the fun you get out of the job. That is, if you're an irrational workaholic, not caring about the consequences of your actions, as long as you get what you want. Not caring, especially, about neither the personal nor the ethical implications of your actions: pretty much the level of self-preservation and morality of a drug fiend willing to hurt both others and himself - as long as he gets his hit right now.
Roark seems to have no preference for what he's asked to build, by whom, for what purpose, for what pay - as long as he's allowed to design it his way and sees it being built, his way. That's pretty much his only two values - designing buildings, and seeing them built.
Well, no, there's a third one. Another sign of his hedonism is undoubtedly the infamous rape scene. The novel suggests that it was Dominique Francon's fantasy - that she was consenting to the whole thing, but simply didn't communicate her consent explicitely to him. But what rational man would want to bet a rape charge on that?
A шаражка architect
Properly understood, Rand's characters are extremes of given characteristics - not actual real life models for full-fledged human beings. This is by design, it's precisely the power of her novels: by applying methodical consistency to characters' values pushed to unrealistic extremes, we can see what those values are. It's the pure definitions of black and white that help us identify shades of grey and which end of the spectrum they belong to.
But those characteristics don't have to be moral values. Sure, an extreme version of a virtue should be a good thing. But enjoying your work, in itself, is neither a virtue nor a sin. There's nothing moral about doing well a job of tax collector or customs agent, or enjoying a useless "work" paid through tax money. Beware of definitions by non-essentials, intellectual package-dealings, and category confusions. A rational person should ask themselves these three separate questions when picking a line of work: is it fun for me? is it moral? does someone pay me for it (and how much)?
What's moral about work is when it is part of a positive sum situation: providing value for value. Work, in itself, is merely anything you get paid for. This does not give it moral value. And in this case it's not actually even work Roark enjoys, it's more like a hobby of drawing buildings.
And he has no moral merit, in it, either. He enjoys it. It just so happens that his enjoyment of it mostly serves other people. Had he had the same passion for, say, designing bombs, he would have made a career in designing bombs.
What if he were asked to design a slaughterhouse? A prison? A concentration camp? What would be his objection towards designing concentration camps, while being in one himself ? Like a шаражка architect : unpaid, uncredited, and toiling for the evils of socialism, exactly like Roark for Cortlandt. Indeed, Toohey understood as much, perhaps understanding Roark better than Roark himself:
Ellsworth Toohey did not look at the plans which Keating had spread out on his desk. He stared at the perspective drawing. He stared, his mouth open.
Then he threw his head back and howled with laughter.
“Peter,” he said, “you’re a genius.”
He added: “I think you know exactly what I mean.” Keating looked at him blankly, without curiosity. “You’ve succeeded in what I’ve spent a lifetime trying to achieve, in what centuries of men and bloody battles behind us have tried to achieve. I take my hat off to you, Peter, in awe and admiration.”
-- Ayn Rand, The Fountainhead
What Toohey means is exactly this: Keating has achieved Toohey's own dream of enslaving creative men to work for no remuneration, no recognition, and toiling for the evils of socialism, against their own long-term interests. Except шаражка inmates were victims, dragged there by force, whereas Roark chose this through his own shortsighted hedonism: Keating's achievement is Roark's voluntary abdication of his own rationality.
A man that lets things happen to him
Voluntary indeed, for Roark did have other options. All he had to do was look for them, instead of merely waiting for others to come to him (movie fallacy #2). He could have drawn plans for a Cortland-style replicable development unit whenever he wanted (don't tell me this sort of design is dependent on the site... this ain't Heller's house), for instance during his out of clients periods, instead of merely waiting for the telephone to ring. Then he would only have had to find an investor among his friends and past clients -- he has them at that point.
Of course, this is what ends up happening anyway:
Roger Enright bought the site, the plans and the ruins of Cortlandt from the government. He ordered every twisted remnant of foundations dug out to leave a clean hole in the earth. He hired Howard Roark to rebuild the project. Placing a single contractor in charge, observing the strict economy of the plans, Enright budgeted the undertaking to set low rentals with a comfortable margin of profit for himself. No questions were to be asked about the income, occupation, children or diet of the future tenants; the project was open to anyone who wished to move in and pay the rent, whether he could afford a more expensive apartment elsewhere or not.
-- Ayn Rand, The Fountainhead
But mind you, at Roger Enright's initiative. Roark, on the other hand, seems to have no preference for what he's asked to build, by whom, for what purpose. He also gaily goes to build for Gail Wynand as soon as Wynand calls upon him, despite what his mentor Henry Cameron told him about the man, despite what Gail Wynand did to him and others -- since when is it a virtue to let immoral people get away with it? Indeed, Roark seems seldom to exercise any rational moral judgment, with the possible exception of Steven Mallory. He admits as much towards Keating:
“Whatever I do, it won’t be to hurt you, Peter. I’m guilty, too. We both are.”
“It’s I who’ve destroyed you, Peter. From the beginning. By helping you. There are matters in which one must not ask for help nor give it. I shouldn’t have done your projects at Stanton. I shouldn’t have done the Cosmo-Slotnick Building. Nor Cortlandt. I loaded you with more than you could carry. ”
-- Ayn Rand, The Fountainhead
And even in his acknowledgement of guilt, he's being somewhat indulgent towards himself: did he ever ask Keating about his real career desires? He knew personally Keating's castrating mother -- did he ever consider telling Keating he shouldn't listen to her, move out and make his own life choices? Was he really thinking that he was helping Keating by ensuring him a fake career in a domain Keating didn't like and didn't choose?
No, of course, Roark was never helping Keating for Keating's sake, or for any higher value -- but merely because he had fun doing it. And why do Keating's projects, instead of some fun projects of his own (or indeed some actual work)? Why because Keating asked him to - again, picking the fun offered by someone, instead of checking his real options and evaluating them rationally and morally. At the very start of the novel, Roark says to the Dean:
I owe you an apology. I don’t usually let things happen to me. I made a mistake this time. I shouldn’t have waited for you to throw me out. I should have left long ago.”
-- Ayn Rand, The Fountainhead
Well, throughout the rest of the novel, more often than not, he does let things happen to him, especially in what's most important to him -- his work.
Roark didn't mind contributing to the reputation of Keating as an architect, even at Keating's expense. He didn't mind contributing to the socialist side in the debate of whether the government or private entreprise should build buildings. He didn't mind bringing into existence a project (after all, they were unable to find an architect until then) that was to be financed through taxation, and which he himself recognized as harmful both to the building industry and society in general.
So through short-sighted hedonism and passivity, Roark entered a dishonest business, government housing, through a dishonest contract: he designed the building, not Keating, that's an objective reality. And then was angry that his dishonest contract wasn't respected by the dishonest people running said dishonest business (with whom he had no contract whatsoever to begin with)? Sounds like someone complaining about consequences of premises they fully accepted.
So unless you want to mount a general defense of blowing up any and all government buildings (with what rational positive outcome expected to come out of it?), there really can be no justification for his actions. If he wanted his contract honestly respected, he should have made an honest contract with an honest businessman to begin with. If he wanted to just blow up government buildings, then still he had no valid justification for blowing that one in particular.
If Roark is quite consistent in his hedonist philosophy of life, Dominique is quite consistent in the opposite: seeking only to hurt herself, hurting others in the process, likewise not as en end in itself, but through sheer disregard for anything but her own goal of hurting herself.
Cynic, pessimist, or cutter?
Superficially, her behavior seems outright crazy. Digging sligtly deeper, it seems as a consistent application of a certain form of cynicism and pessimism that we all commit on much milder levels. Her pushing it to the extreme shows us how it's a bad principle to begin with. Yet digging even deeper, there's something else: consistent cynicism and pessimism don't actually imply being part of the problem.
Like Roark not minding being part of the problem as long as he gets his fun, Dominique doesn't mind being part of the problem as long as she gets her suffering:
“You’re not aware of them. I am. I can’t help it. I love you. The contrast is too great. Roark, you won’t win, they’ll destroy you, but I won’t be there to see it happen. I will have destroyed myself first. That’s the only gesture of protest open to me. What else could I offer you? The things people sacrifice are so little. I’ll give you my marriage to Peter Keating. I’ll refuse to permit myself happiness in their world. I’ll take suffering. That will be my answer to them, and my gift to you. [...] I will live in the world as it is, in the manner of life it demands. Not halfway, but completely. Not pleading and running from it, but walking out to meet it, beating it to the pain and the ugliness, being first to choose the worst it can do to me. Not as the wife of some half-decent human being, but as the wife of Peter Keating. And only within my own mind, only where nothing can touch it, kept sacred by the protecting wall of my own degradation, there will be the thought of you and the knowledge of you, and I shall say ‘Howard Roark’ to myself once in a while, and I shall feel that I have deserved to say it.”
-- Ayn Rand, The Fountainhead
Now I know the usual interpreation focuses on the pessimism of the start of the passage, but let's dig deeper:
"gesture of protest": towards whom? who's gonna know about it? who's expected to change his behavior as response to acknowledging her protest?
"What else could I offer you? [...] I’ll give you my marriage to Peter Keating." offer? this has no value to anyone, it's not something to "give". (Unless Roark had expressed such a sadistic desire; that is not the case.) The only result is to hurt all three people concerned -- the rest of the world couldn't care less.
"refuse to permit myself happiness in their world": you mean, hurting yourself with no benefit for anyone else, either? you expect a badge of merit for that? granted by whom?
"the world as it is, in the manner of life it demands": "the world" doesn't "demand" anything. There are simply some people who have expections of you that match your own values, and some people who don't. The rational thing to do is to associate with those who do -- unless you're a second-hander who wants the love of "everyone", and is irrational enough to consider it possible? There is no "official world stance", no "official" recognition, and especially, no official medals granted by "the world" for those who do what "it" demands. Because seriously, that's pretty much what she seems to be expecting here.
"kept sacred by the protecting wall of my own degradation" wtf?
- "and I shall feel that I have deserved to say it" deserve? hurting yourself is not a virtue and does not make you deserve anything. Pain is not a virtue. Sacrifice is not a virtue. Unhapiness is not a virtue.
The lesson from it
We see that Roark and Dominique are quite the polar opposites, focusing respectively on his own fun and her own suffering. What they have in common is a certain consistency in seeking these aims.
But consistent doesn't mean rational: it depends on what the premises are. Yeah, them premises Rand says you oughta check. There is no rationality in being consistent with an irrational aim. There is no virtue in being efficient and uncompromising in hurting yourself and others.
What both seem to be sorely lacking is a better understanding of philosophy, especially about the morality of their actions -- a necessity which Ayn Rand would explain in Philosophy: Who Needs It, and provide to her next characters in Atlas Shrugged.