You do what the person with the gun says, because you believe they'll shoot if you don't. If you believe that they will shoot and kill you regardless, following their orders is (at best) going to give you a few more agonizing minutes to live. The threat becomes meaningless.
Don't try to overpower the hijackers? You die. Try to overpower the hijackers and fail? You die. Try to overpower the hijackers and succeed? You live. It only takes one person to do the math and realize they are basically in a no-loss scenario.
Yes, the math is the easy part, doing is the hard part. The difference between understanding and doing is large and denial, shock, rumination, and rationalization all fuel inaction and there is often a moment in which it becomes too late.
People on death marches, in concentration camps, or other similar scenarios have the same math, and yet they get gassed or forced to dig their own graves after which they are shot and buried in them.
So yes, rationally that all makes sense and we should celebrate anyone putting themselves at risk to fight for the benefit of a larger group, but reality is different, especially if the hijackers can guarantee at least one death.
To say a hijack could never happen again is wrong. The doors are a much more reasonable explanation than the courage of men.
History also gets forgotten, such as the history of secret police or mass deportation efforts as is quite clear in this thread.
Assuming something is true doesn't make it true. Colluding airport employees as well as rural airports seem like clear vulnerabilities. When thinking about security problems you don't just assume your security measure always succeed and assuming that all passengers are "equal" seems like a poor assumption, especially for an exceptional case by highly motivated people, potentially with state backing.
Don't try to overpower the hijackers? You die. Try to overpower the hijackers and fail? You die. Try to overpower the hijackers and succeed? You live. It only takes one person to do the math and realize they are basically in a no-loss scenario.