Very good topic. However, could it be broadened to general bigotry? Because there's a lot of racism among anime/anime fans as well, and most of that isn't even noticed. Like if a girl asks who she looks like, and the girl is black, everyone says Anthy even though a--the girl may look nothing like Anthy and b--Anthy isn't black anyway, she's more Indian. Granted that's not RACISM OMG but it's more pigeonholing, especially given that most Americans who cosplay anime characters are white rather than Japanese or even any sort of Asian.
But yes, a lot of yaoi fans have noticed homophobia even in our own ranks, fetishizing it and demonizing people who really *are* gay. It happens in yuri as well, and that's even more ingraned.
Another thing that gets me is hetphobia. I mean seriously, we ALL came from het unless you were born in a lab (even test tube babies are the result of het SOMETHING).