I may be wrong... but....
Depending on the size of your raise, he may have had a pocket pair and was set-mining, so 22 or 33 is a possibility (22 is very unlikely, but not impossible). He may also have had a middle-pocket pair like 66-99 and as the flop is ridiculously low felt that he's ahead and decided to apply pressure. If he was slow-playing, feel free to cut his genitals off with a plastic spoon - painful!
That said, given that the highest card on the board is a 3, he maybe sensed your cbet was a bluff and decided to check-raise to apply some pressure or test whether you had a higher pocket pair.
I'm a nit, I'd fold with AK to a re-raise... but would be interested in hearing of more adventurous (and probably better) lines to take.