I'm a heterosexual male, and I would have no problems at all with a homosexual main character in a Final Fantasy. As long as it was handled right, it would have the potential to be very interesting. I would love to see what they would do with the story and the themes that they could inject into it. But, I doubt a large number of gamers would take this very well.
It's for this reason, that I don't think it will ever happen. Not in a million years, unless a large number of peoples attitudes and opinions take a drastic change.