Pilots are busy flying the airplane, how can they be expected to defend their cockpits as well?
As captains, we are charged with prioritizing problems and dealing with them in a logical order that ensures a safe operation. In fact, our training is concentrated on making us experts in crisis management. Whenever an emergency exists, standard airline practice requires the captain to designate a pilot who continues to fly while the other devotes his attention to handling the emergency. Just as we train for combating onboard fires, so would we train to defeat a cockpit intrusion. If terrorists were breaking down the cockpit door with the intention of murdering the pilots and using the airplane as a bomb, all would agree that this is an emergency of the highest priority. If the pilots do nothing to stop the attack with finality and simply continue flying, they will soon be dead, as will all of the passengers, crew and possibly thousands of citizens on the ground.
