3BB is not enough at $25NL to push out low pocket pairs. Depending on the table, 6BB is not enough if that's what you are trying to do. On the flop you said you bet 1.25 (about a pot bet), that was good. When he re-raised you to 5, what do you think he has? Top Pair?? At $25NL, most players aren't crafty enough to be sneaky with their monster hands, and if he thought you had an Ace here due to your preflop raise, he's trying to push you away from drawing the straight. He'll be happy to take the pot down here when he knows that he's in the lead most likely.

At this level, I give credit for a Set (or possibly a fish with A3 that got lucky) and I fold my QQ EVERY time to this flop re-raise. If he shows me his cards and that he bluffed me out of a nothing pot, I make some notes and take his money later...