It seems to me it was obvious you had a big hand... I don't know why he wouldn't have check raised on the flop. Yeah, he could have scared you away, but raising the amount you bet probably wouldn't have shaken you off those A's. In fact I find it difficult to believe that he would have been able to shake you off of those Aces at anytime. A rainbow flop with one high card makes it hard to lay down Aces. Especially when you raised to $16 preflop, he should have a decent hand. I wouldn't have put someone on pocket 5's or 3's either. So at that point, you're betting he doesn't have pocket Q's, b/c you know he doesn't have two pair.
So yeah, I might feel a little dirty for sucking out, but not so dirty I wouldn't take his money . Besides, you had a great starting hand, and I think you played it correctly. I would have played his hand differently, but I would have also lost more money.