It has been in some games, like the ones already mentioned, but i think the main problem is that if a company made a game in which the main protagonist was openly gay, they would have to contend with the media outcry.
Most companies probably don't see the need to make such a controversial game and risk a lot of money, face and possibly loyal customers in a game that could be banned for its themes.
I'm all for gay rights, and have several gay friends, that all seem to think that homosexuality is represented in movies and video games subtly, so that it is in the game but not a massive controversial point and hope that through this subtle media input that one day there will be an openly homosexual protagonist