Well if I call and hit blank on turn, then I have a very strong hand that has now become a lot weaker. If he double barrels the blank turn, I then have no fold equity on the turn, and I'm probably not getting the odds to call his bet.
I do occasionally play draws the way you suggest, but I think it's ok to mix it up a little FP.
By playing the way I have I'm building the pot to a pretty good draw + I also have a fair bit of fold equity as well.
Last thing first: I'm not saying that raising the flop is awful, not at all, but it seems you were "surprised" by him 3-betting (in the sense that it put you in a tight spot), which suggests that perhaps you hadn't thought your raise through.
Now, regarding your first paragraph, your reasoning is correct, but your conclusion ("don't call") isn't. Look at the four things that can happen if you call:
1. He checks the turn, and
a) you miss your draw. You can take the route of semibluffing now, or you can check behind for another free card to the nuts in a small pot with 100BB stacks. You're probably not going to win a big pot, but if he had nothing in particular on the flop, chances are pretty big he'd have folded to your raise anyway and you would have ended up with a 11BB pot.
b) You hit your draw. You have position; bet away. You might only win a small pot, but the same reasoning applies as above; he probably didn't have much anyway so the pot you win is usually the same as if you had raised immediately.
2. He bets the pot on the turn, and
a) you miss your draw. Now, understand that a pot-sized bet is only 14BB here. You still have 80BB behind in your stacks. While you're only getting 2:1 on your call (and you'd be 3.4:1 vs. AA), you only need to make up $20 on the river when you make your hand. In position, this is of course not a problem.
b) you hit your draw. You said you have no fold equity, so push away. Grats you, putting in 80BB as a 77% favorite as opposed to a cointoss.
A good reason to raise the flop is to fold out 88-KK. However, these hands don't generally bet two barrels (in my experience) and your fold equity is probably as good on the turn as it is on the flop. Also, if he shoves the turn (90BB into a 14BB pot) after you call a tiny bet on the flop and you miss, then it's unfortunate, but I also think you have to agree that that's a bit of a freak occurence.
Out of position, however, I raise this every time, since I want to nullify his positional advantage. But when I'm the one with the advantage, I'd rather keep it - generally speaking.