top pair on the flop vs. 3bet on flop

Live $1/$2. When villain 3bet more than half of his stack, I had no reason to think that villain wouldn't put the rest of it in, if I raised here or once turn is dealt. Most of villains range consisted of two pair (most likely A5) and sets. I thought hands like 99-JJ would just call, and most aces would call as well (AK would probably 3bet pre flop), so I didn't think that in the long run that I would be profitable once stacks got in the middle. Do you agree? Thanks