It's entirely possible it's not the right course of action, but it's reflex. Now that it's known terrorists view aircraft as weapons, even taking control of the aircraft is a deadly threat.

The weapons usually used to control an aircraft are the threat of bombs. A fake bomb is just as effective as a real bomb, and vastly easier to bring onboard, so it seems rational to presume any bomb threat is fake. To a first approximation, hijacker in a plane aisle is a problem of running at him and tackling, which is about the easiest possible thing to do.