Are you destine to lose a big portion of your stack in NL when you play AKs out of position and your heads up, and your opponent catches a set when you catch an A or a K in a raised preflop pot?
Well...who did the raising?

If you did (which I would with AK, position be damned), and he calls you preflop, but raises on the flop -- even if you catch an ace -- you might give him credit for having called with a pair and flopped a set.

Then again, many players will raise pre-flop with ANY pocket pair -- especially if they have position. And many raisers will continue their agression after the flop, even if they miss. It all comes down to what you put the guy on initially, based on how you've seen him play.

As everyone else has said (in some form), if you think you're beat, lay it down. If you've got TPTK and think you're up against a set or two pair, that shouldn't be a hard decision.