Even though it is mathematically correct to call an all-in with TPTK or an over pair when you are certain the villain is on a draw, do you?

For example, you hold Qh Qd and the flop comes all low cards with 2 diamonds.
You lead out, Villain goes all in and you are better than 90% certain villain is on a flush draw.

Do you call or fold?

Assume effective stacks were 100 blinds pre-flop.

Say the flop comes 963

Reasonable flush draw combos:

A2 - AQ (9), K9 - KQ (4), QT,QJ, JT,J9, T9,T8, 98,97 87,75, 54 = 24 combos

There are 9 set combos

You are never going to be 90% sure

Still it depends on some other stuff. Probably best to post an example hand

Right. I don't know how you can be certain, because a villain that will shove with a FD will also shove with a set/2p/AA/KK for balance, if shoving makes sense (i.e. you guys aren't effectively deep stacked). If you are deep stacked, then shoving a set doesn't make as much sense, and I would think a raise might be the plan of a solid player, hoping you shove. But a weaker play might easily raise/shove a set deep.

That all being said, I don't think a call is terrible against an aggressive player assuming the pot is raised/3bet pre. This flop really doesn't give him much 2P combos, and even sets might be few and far between if you were the one 3betting pre. Post more info next time.

If you are certain something is mathematically correct, why on earth wouldn't you do it?