I'm curious why you put him on a set so quickly. I'll raise and c-bet quite a bit when short-handed, especially from the button. If you don't, then he probably believes that you have a Q, and you should fold. But up to the raise on the turn, I'd play the same way with AK, just about any pocket pair, and maybe a few others. My first guess is that he doesn't believe you have the queen.
Would this be a good time for a blocking bet on the river? As is, I'd probably call the river bet. Without knowing more about how you and villian have been playing, I think you're ahead.