Sometimes it's actually optimal to keep the shortstack alive.. but yah.. I know what you mean when you see some donk bet POT when he flops mid pr on the turn.. meanwhile you're on a good draw.. he bets you off the hand and shortstack triples up... donk!!! frustrating.
Other times it's optimal to keep the shortie alive. Here's an example. You're C.L., you're on the bubble (of mtt or sng) and by keeping the shortstack alive you can continue to pound on the other's blinds or once in a hand with them, put them to the test for all of their chips (pressure the hell out of them). Of course they're going to have to have the nuts to make the call cuz buddy over there is sitting on a shortstack (although I've also seen this go the opposite, CL folding, then as sb with QQ shoving onto bb who is the other mid-sized stack and having him call with K-2, risking his tourney life???... why??. and having him hit the King and end up going out on the bubble).
Other than specifically trying to keep the shortstack alive to take advantage of being the C.L., I can't offhand think of other reasons that someone would want to bet you off a hand. If I'm in the hand with a good player, I'm going to trust that he's flopped a set or turned or rivered a nutflush or something. With many players though.. you just never know.. there are many who are clueless.