Dagney is a strong woman, strong character. She conquers anything she sets her mind too. The train ride is part of this sex scene. Her train, Readon's steel. Is it really rough sex or passionate sex between strong people? If Dagney had said, "No." Hank would not have violated her.
I think the sex thing is more than just Dagny’s character. I think a lot of it is Rand herself. If you read The Fountainhead, Dominique Francon has pretty much the same sexual appetite as Dagny and the scene with her and Roark by the quarry is one of the most important of the novel. You say Rearden would have said no, but Roark didn’t, and Rand clearly approved of Roark.
Even We The Living, which is her first novel, and not really as philosophical and more traditional that Atlas and the Fountainhead, has a main female character in Kira who also has hot, rough sex. I even read a book that has a bunch of short stories written by Rand and unpublished stuff and it’s there too.
I think Rand pretty much wrote the main female characters(Dagny, Dominique) with a lot of herself in mind and they’re having wild, animal sex with the male heros and ideal men like Roark and Galt and Rearden represents her desire to the same. Just her own added fun to the book. The rough sex is probably how she liked it and if you read some of what Branden and others wrote, it’s no surprise.
I don’t relaly think the sex is all that important in the overall philosophy. It’s like in spy novels like Bond or a bunch of others where a male author has his hero have hot sex with a bevy of babes. Don’t foregt she also began her career in Hollywood so she probably still retained a touch of the romantic and the show in her later works. It’s like if there’s a movie out about serious things but it also has a nude scene with Angelina Jolie or Kate Winslet, it’ll draw a bigger audience. See The Reader, for example. I mean, she was intimately involved with the film version of The Fountainhead and casting and picked legendary swordsman Gary Cooper as Roark. No coincidence there.