I've seen it a lot, hell I've even seen a guild website say "no girls allowed because we're hardcore." I don't remember which guild it was, I think it was a top 200 guild though. It's there, you're just fortunate not to have seen or heard it.
I helped run a small guild, filled with friends. We would have anywhere from 2-5 girls on the roster at any moment. People were mostly well behaved, except this one guy that was always a pain in my ass. I had raided with him off and on for something like five years.
This one typically quiet girl in the raid (who was also one of the best players in the guild) seemed to be friends with him early on. Years later, she seemed to be egging me on to kick him out of the guild. This seemed really bizarre to me, since I thought they were friends, but I kept him around because I was too goddamn lazy to recruit anyone.
Fast forward to some guild drama involving him and another girl, where he demanded she be kicked from the guild. Long story short, after he left the guild when we refused to kick her the stories came FLOODING from all the girls that ever played with him. He was a huge creep, [tried to be] manipulative (he wasn't bright), and crazy sexist. They all hated playing with him because of the type of stuff he'd whisper to them.
Honestly, some of the fault lies with me. I was sort of an apathetic leader, but none of this stuff really came to surface publicly until after he left. One of the girls I raided with went on to lead a raid in another guild, and I did a couple runs with her. The sort of stuff said to her face over Mumble, even if it wasn't technically serious, was uncalled for. People put up with some pretty nasty stuff just for the sake of civility.
One last short story: I lived in student housing with a randomly assigned roommate before, and he was one of those guys that would shout obscene things over Xbox live. Easily the most sexist, homophobic, and racist person I've ever met in person. We fought a lot. He ended up getting his ass thoroughly kicked by some guy at a party.
I'm not a violent person, but that shit made me laugh.