As the world at large (save a few places) gradually begins to accept sexual preferences as two things: 1: not defining of a person's character and 2: none of our god damn business, it's not surprising that homosexual or otherwise characters will show up in books, movies and potentially even games more often than before. However they're still far from common and specifically so in the latter.
The reason behind that, according to openly gay Ubisoft lead writer Lucien Soulban (winner of most badass name three years in a row) is because publishers would be worried of negatively impacting sales. Because of that, he believes it'll be a long time before we see an openly gay lead characters in any big AAA games.
"Either we’ll see a bait-and-switch like the original Metroid with Samus Aran where we’ll find out damn near after the fact (PS: And Dumbledore was gay), or it’ll come out of left field with Rockstar, Valve, Naughty Dog or Telltale, perhaps," he said in an interview on Ubiblog. "But when it happens, I hope it’s a serious take on it and not played up for jokes."
More likely he thinks, gay characters will come about through player choice, rather than being written that way.
"Look at the choices offered in Mass Effect II & III, or Fable III, or Dragon Age II or Skyrim, the gay characters in Borderlands 2 who mention it without much fanfare, etc. Videogames have stopped “announcing” gay characters. They’re introducing them without much fanfare in an effort to say, Yeah, it’s there and pretty normal. Call it: We’re here, we’re queer, and we’re busy working."
The ironic thing with putting gay characters in games or movies, is that their sexuality is very unlikely to come into play, unless it's through Mass Effect like relationships. Because really, it doesn't matter what someone does with their genitals or who they fall in love. As long as they can save the universe, who cares?