Not a flight attendant, but I would guess it depends on the reason for the applause. If the passengers are being deliberately sarcastic, that is, aiming to imply that the crew's performance during the flight was so incompetent and irresponsible that making it back onto the ground all in one piece was a minor miracle, then certainly any applauding ought to be taken as an insult. But maybe the intent is to show sincere appreciation, in recognition of how tough it can be to work in the skies these days; perhaps during the voyage the crew skillfully handled a medical emergency, subdued a berserk wannabe terrorist, broke up a drunken fistfight among God-knows-how-they-were-allowed-to-board fellow passengers, or picked up the pieces after a terrifying bout of clear-air turbulence. And if they did so while maintaining courtesy and professionalism toward everyone on board, I can't imagine a round of appreciative clapping would be inappropriate, but then again I'm not a frequent flier and thus not attuned to the customs and protocols of air travel.
In my former profession, there used to be
a tradition of applauding professors after a lecture, or at least at certain august institutions. It rarely happened to me, but when it did it was usually because the drone of my monotone lulled my student audience, most of whom were still abysmally hung over, into blissful, feel-no-pain torpor for a merciful hour, and when they awoke they reciprocated like zombie seals: