Most hostage situations (even on airliners) end with the hostages going home safely. It's rare to kill a hostage and almost unheard of to try and kill everyone.
The only analogy I can think of is a robbery; if it's clear all they want is to get the money and get away, you're probably best served by complying but watching out for anything indicating a more imminent threat of death. If you can tell, though, that they are going to kill you, you might as well fight.
The passengers on Flight 93 accepted that they were already dead and fought to save the lives of others. They did good.
The passengers on the other flight (except the Pentagon strike) probably didn't know. I can't fault them, given that they were raised to comply.
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