Have you looked at he may possibly be holding Q9, QA, JT, or KJ?

I put him on maybe KJ at best. He maybe also on a QA offsuit as well. Even if he was on a flush draw, you should push a 2/3 pot bet on the flop as it won't be worth it for him to call if (like in this case he would'nt of hit it).

Also your bets are not even half pot bets.