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So you would never just call a bet from somebody you had position on, with a nut flush draw on the flop? You would always raise?

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There are not "always" or "never" moves in poker. Sometimes the situation calls for a raise, while others call for just a call.

In the hypo you set out (1 bet, 1 fold, your turn to act with 2 players yet behind you), I like raising for the free card. The original better is 99.9% sure to call your raise, as people who bet on the flop rarely fold to a raise. By raising, you will more than likely get the 2 players behind you to fold, opening the door for taking a free card on the turn if you like.

One exception to this recommendation might be when either the flop is coordinated (7-8-9 for example) or all random low cards (such as 2-5-7). For the low-card flop, depending on the players at the limit you play at, people in later positions will call a bet and a raise with any 2 big cards, figuring that such an "ugly" flop couldn't have helped anyone. So you have to figure out if the players behind you are likely to fold to your raise.