I say this with no disrespect to the memory of passengers and crew of those planes but when faced with this sort of situation the stress and bizarre horrific atmosphere often shocks people into a passive stance.
It was frequently seen during the holocaust and other horrific events that people who would normally fight back don't.
These behaviour patterns are covered by the unfortunate umbrella term SEP (Somebody Else's Problem).
Essentially a variety of points of view come to play where a group of people do not enter a fight for survival stance.
Some people assume some outside agency will save them and taking personal action would only make the situation worse (not just for themselves but also for the other people in the group).
Other people assume that taking action would be pointless.
Other people wait for a sign of leadership within the group which they can rally behind and will not be the first to act.
We also need to remember that up until this point hijacking a plane and turning it into a missile was unheard of, almost every hijack situation had ended in passenger survival.