I think you want to raise the turn for metagame reasons. No, seriously.
By flat calling his ridiculosly small bet, you are kind of letting him set the tempo. With a big hand (3rd set on a AQ9X board), you then forfeit your right to bluff raise a tiny turn or flop bet in the future.

Of course, it could (always) be an elaborate trap to get you to raise into AA or QQ.

In a vacuume, I think you played it fine because it's quite possible he has an even bigger hand, and not getting stacked after flopping a dominated set is quite a coup.