I'm pretty sure that by showing weakness on the flop and the turn he wasn't sure if I had a hand better than QQ, and he decided to call such a small raise on the river to look me up/keep me honest. I'm pretty sure had I went all-in he wouldn't have called, deciding instead that it was too much money to risk his stack on. Plus with that potential flush out there on the river, he very probably could have been scared off by an all-in bet after it looked like I had been drawing for two streets.

Look at it from his perspective. If you're dealt QQ and your opponent shows a lot of strength pre-flop but then checks the flop when an ace shows, you bet a very small amount and he merely calls, the turn comes, shows a king, he checks, you bet a very small amount, he merely calls again, what hand do you honestly put him on at this point?