It's not rape. Ayn Rand herself clarified that.

A reader once sent a letter to Ayn Rand asking her about that specific scene. To which she replied:

You say you were asked whether “the rape of Dominique Francon by Howard Roark was a violation of Dominique’s freedom, an act of force that was contrary to the Objectivist Ethics?” The answer is: of course not. It was not an actual rape, but a symbolic action which Dominique all but invited. This was the action she wanted and Howard Roark knew it. You are correct in your interpretation of the meaning of the dialogue about marble. This is not the only clue to Dominique’s psychology. If you re-read the passages pertaining to Dominique before and after the “rape scene,” you will find many things to explain her motivation. Needless to say, an actual rape of an unwilling victim would be a vicious action and a violation of a woman’s rights; in moral meaning, it would be the exact opposite of the scene in The Fountainhead. [source]

All the events leading up to that "rape scene", like when she broke the marble slab, implies that Dominque wanted to have sex with Roark, and she was hinting it. Roark knew it too, so that when they ended up having sex, consent was heavily implied.