Stanley Kubrick did. David Lynch did. Alejandro Jodorowsky did. Mel Gibson did. Quentin Tarantino did. Hitchcock did. Sergio Leone did. Trey Parker did. Seth McFarlane did. Ridley Scott did. Akira Kurosawa did. Clint Eastwood did. Oliver Stone did. Frank Miller did. Alan Moore did. Zack Snyder did. Elem Klimov did. Try looking at the keyword "rape" on imdb.
Did you know that there's rape in CSI, Criminal Minds, The X-Files, even Little House on the Prairie?
There's countless of people who create things involving rape. Not a whole lot of games. Rape is a real world problem. Even the depiction of it in fiction is, which I think everyone here has understood.
You are free to think that the games I make are trash, or that rape is something that should not be in games, or that specifically in our game it's handled poorly. I won't argue with your personal opinions, how could I possibly decide how you feel about something?
I personally avoid things I know contain "rape scenes", I have a hard time watching films with unprovoked violence, and I don't think rape is something that can be justified as an act done to another being. So I can perfectly understand how people are feeling about it. If I didn't find the subject upsetting, the sequence in Hotline Miami could have easily been a lot worse. However, there are times when I feel that it's justifiable to depict rape in entertainment/art, if it's within a reasonable context.
The main problem for me in this situation is that I have doubts people will try (nor succeed) to understand what the scene really means, and I have no desire to explain things I want people to figure out on their own. I'm not sure everyone would approve of it even if they understood it. This makes it harder to justify the inclusion of the scene in the game.
To me, Paul's suggestion of having an option to "turn it off" before playing the game seems reasonable. I don't mind if someone feels bad or is disgusted because of our game's content, but I don't want people to have a traumatic experience playing the game.