Pre flop bet size was likely too small to chase off weak holdings.
I actually ran into a similar situation last night at $200 FR live with AA on the button, the table suddenly got a lot tighter and people weren't getting action with $10+ PFRs, mostly folds to me so I make it $7 to see whats up, cutoff insta calls on a 574 flush draw board, I bet pot, he calls, turn gives me a set of aces, I bet 3/4 pot he doubles it, I call hoping to fill up on river with a boat,, river brings flush and more straight possibilities and no boat for me. I check because I'm beat here, he bets like 1/2 pot, I fold but show my hand, he smiles and shows 36o for the flopped straight. Had I bet more pre flop he would have likely folded and I while I wouldn't have had any action, I would've taken blinds and saved myself money.
So as others said he probably flopped 2p, a straight, or most likely a small set because he got in cheap. Fold the his re-raise on flop. Yeah there's a chance he has like 99-JJ but you can't be sure. If the pre flop raise you made was like $10-12 he might let go of a small PP or ATCs and if he called you could put him on something like 99-JJ because if he had KK or AA he's probably 3 betting you pre anyways.
I know if someone makes it that cheap to see a flop I'm probably calling to see, yet I made the same mistake you did.