Haven't all cockpits now become much more secure? I'm no expert, but it's my understanding that the pilots can seal themselves inside. Anyone trying to get into the cockpit would become a sitting duck, even if they were ruthlessly executing passengers with their simple weapons, 50+ people (likely including an air marshall or at least a strong, fit, high level athlete) should be able to overcome the hijackers. Post-9/11, I doubt many people take the "I hope they don't turn the plane into a missile" route.
Short of getting several automatic weapons on the plane or some kind of chemical weapon that can kill or incapacitate everyone on board, pilots being able to seal themselves off, coupled with internet and cell phone access getting better seems like it would make a repeat 9/11 extraordinarily difficult.