Here's a thought on improving the security of the planes themselves:
How about installing a time-lock of some sort on the controls, so that once the plane is airborne, only the ATC on the ground can release the controls back to the pilot once the plane is approaching its destination?
Yes, yes, of course there would have to be failsafes in the event of an emergency, but if a system like this were in place, wouldn't the fact that the pilots CAN'T direct the plane deter hijackers?
Shouldn't all new planes be built so that they can only be flown by remote, or at least have the manual controls and the pilot present only as a backup to the remote pilot? Remote-pilot-vehicles are a fact, the military uses them as battlefield reconaissance drones. If we're worried about pilots being replaced by terrorists, let's remove the pilots from the equation altogether. We all know that planes can be landed by wire, and landings are arguably the most dangerous maneuvers a plane can make, it is deliberately approaching the ground. If a computer can land a plane, why not have it do the takeoff, flight, and landing all the time?
Decent anti-virus software and a firewall will eliminate cyber-terrorist concerns. Hell, make the robo-pilot an independant system, monitored only (when I say monitored only, I mean it tells the other computer what it is doing, and communication is one-way) by another computer that is in contact with the ground. Then no one can mess with it, except the pilot on board.
The details of the system (like how many backup robo-pilots are in between the main one and the human pilot in the event of an emergency) can be worked out by the designers. The technology exists, let's use it.
What do you think?