When you say "with" I assume you are asking why she is his girlfriend. I assume that you are thinking that she is a nice kid who seems to actually like some of the greasers like Ponyboy. So, you might ask, why would she want to be the girlfriend of a violent and nasty guy like Bob?
The reason is because of what she sees in him that others do not necessarily see. To her, he is a special person. She thinks that he has a quality of leadership, of charisma that most others lack. She thinks that this is why other guys will follow him. That attracts her to him even though she knows that he is not perfect.
In addition to this, she says that Bob has another side to him. She says that he really is a pretty nice guy when he has not been drinking and when it is just the two of them hanging out.
When Bob died, she told Pony that he was a 'special' person. Randy told Pony that he just wanted a no from their parents but they wouldn't. Bob might have been a great person that Cherry fell in love with but had a bad/dark side. He got drunk most of the time since his parents are too nice. Starting fights with greasers which happens to be twice for Johnny.