Currently released RPGs that feature an optional homosexual male hero (that I can think of off the top of my head):
Jade Empire
Fallout 2
Obviously the fact that you could marry a guy in Modoc didn't hurt Fallout 2's reception, so I don't quite thing that the presence completely offends people.
Actually what is a little disturbing and saddening is comments that "It's okay if the hero is gay, he just can't have a relationship at all." More or less they'd rather the main character be Asexual or just the "sissy" archetype than actually be gay.
Take a look at John Barrowman, Scottish actor, plays Captain Jack in both Doctor Who, and in Torchwood. The actor is gay and the character is... for the best word, pansexual. Does the fact that he kiss men, and wake up next to them naked make him that much less of a badass when he's blowing aliens away? Besides, a person's (or character's) orientation isn't who they are, it's just an aspect (unless you look at a lot of one dimensional character coming out of most games these days.)
In most FPSs, is there really a point to add character sexual orientation? No. Gordon Freeman is just an avatar of the player, more of an avatar of any other FPS hero as we never see anything but what his eyes do. The Marine in Doom is just "Generic Gun Toting guy no. 7242." Duke Nukem is simply Ash from The Evil Dead shoved inside a blonde 2D platform hero. The Postal Dude is just some schmuck who has some errands to run.
Puzzle games? Nope. Platformers? Maybe, but not necessarily. Sports games? I doubt it. Really, only story based games (which primarily rely on RPGs, but Kojima, Rockstar and a few others expand on that) are the ones that sexual orientation might actually be mentioned, same for race, sex, religion, education, and other things. Most of the time, the hero is simply a blank avatar for the player.
But in the end, as I said before, orientation isn't a person, it is simply a trait of their being. I might be a college student, a gamer, an American, a voter, a cynic, an employee, and, in fact, a homosexual, but they aren't me. I'm me.