The other thing that prevents another 9/11 is the first 9/11.

Before 9/11, airplane hijackers were like bank robbers: idiots trying to get some cash. If you just followed their orders, everyone would mostly get out alive.

Even mid-9/11, when it became clear that the hijackers were using the planes to attack civilians (at the necessary cost of the lives of the passengers), people stopped cooperating and stopped the final plane from reaching its target.

Even if someone walked into the cockpit with a gun they'd get nothing for their trouble but an immediate nosedive as the pilot sacrificed the plane to protect whatever the intended target was.