I think, if a game came at this from a sincere angle, that there would be very little problem with a homosexual protagonist. The biggest hangup is doing it in a way that isn't superfluous or insulting. To draw a parallel, look at how many games have female protagonists... that aren't just doing it for the spectacle. They're distressingly few. The problem you get, especially in an industry so dominated by corporate funding, is that you have a writer who (in addition to being less than comfortable when it comes to writing in say, the female voice or the homosexual voice) is heavily pressured by the people who write his paycheck to perform to their standard. So the finished product comes out as:
Bob: "Hi! I'm Bob. I'm gay."
Bob:"Look at me, being all gay over here. With my drag and my funny voice and my love of men."
Bob:"Teehee... gay..."
Bob: "Hi! I'm Bob. I'm gay."
Bob:"Look at me, being all gay over here. With my drag and my funny voice and my love of men."
Bob:"Teehee... gay..."