I think the problem with a gay main character would involve the game company trying to milk it. They would likely expect a great deal of controversy, as well as publicity. And there's no such thing as bad publicity. So the game companies start milking it for all it's worth. They make press releases about it, they emphasize it on game posters, basically saying "HEY, LOOK EVERYONE! THE MAIN CHARACTER IS GAY!!!" So, the game finally is released, and the main character is gay. Um... what now? Where do we go from here? What I'm trying to say is, the hype would imply that the character's sexual orientation is central to the story, even though it wouldn't be. If the main character was black, would that be the center of the story? No, unless it was an RPG set during the Civil Rights Movement or the Civil War.

In short, while there's no real reason to have a gay main character, there's also no real reason to not have a gay main character. I would prefer if it wasn't the focus of the story.

And now I'm gonna get a bunch of people jumping on my ass about how I'm a homophobe.