I don't really read rape stories so I can't recommend any, but there is a rape tag in mangaupdates and novelupdates. A lot of wuxia has men raping women who then fall in love with them.

Most shoujo manga stories feature a female protagonist, who are also the victims of the rape, but they eventually like it. That doesn't fit what you want though.

The idea I was trying to present is that rape isn't as censored or rare as you think, and there are a lot of stories where rapists are redeemed or even praised (because the girl deserved it kind of thing).