($22) - Level 1, Protecting Aces on a friendly monotone flop?

[SammyKid11]

Level One - 10/15
Hero UTG+1 (775)
Villain in SB (645)

Hero opens for t50 with AsAd...folded to SB who calls, BB folds.

Flop (2 players - t115): 9sQs3s
Villain bets t55, Hero raises to t200, Villain folds

Alright, so I made a standard large raise to "protect" my aces from the flush (though I did a crappy job of attempting that since I left him with proper odds to draw). I then, however, just sorta "realized" that if my opponent was drawing to a flush, he was in big trouble because I had the ace of spades. My opponent either already HAD the flush (in which case cheap cards would help me) or he was drawing to a second best hand (in which case letting him hit his second-best flush would be very profitable)...maybe he has a QT or something, possibly with one spade, and I need to protect against trips or two-pair. I'm confused here, though, so please let me know what you'd have done differently in this situation.