I've got a whole long blog post brewing on the subject in my head, but here's how I see it:
Fundamentalists aren't going to go away but they're going to change. In a generation, gay rights and gay marriage will be as widely accepted as minority rights and interracial marriage -- some people will still object to them, and some of those will object strongly and vocally, but most homophobes will act offended when you call them homophobic just as today most racists will act offended when you call them racist.
They'll do what they did with minority rights: they'll wrap their discrimination in euphemisms and attack things that are RELATED to the subject but totally not the same thing.
And they'll find a new minority to openly discriminate against.
Who that's going to be is anybody's guess. Transgenders? Polys? Indians and Chinese? (Not because of their race, of COURSE not; because of their ECONOMIC POLICIES!)
Hell, they'll probably even pull the same historical revisionism they do today with all the "It was the DEMOCRATS who were racist!" half-truths. "Hey, Barry Goldwater SUPPORTED letting gays serve openly in the military; BILL CLINTON pushed Don't Ask, Don't Tell!"
Round and round it goes. When it's no longer socially acceptable to hate one minority, they find another -- and claim they never hated that first minority at all, that was those OTHER guys!