I agree with rpm in that I don't think checking this flop was bad, i just like betting more..

it may make weaker hands that wouldve folded the flop call a turn bet, and give AQ more confidence in his hand as he may place you on JJ/QQ.. you may also induce flop bluffs form pp's that aren't 99. The best play is likely dependent on player tendencies but you don't know what they are so its better to bet than to slow down i think