"I do not need a gun to protect my flightdeck, but you definately need one to convince me to release control and the bullet would have to enter my scull to make me."
P7lot, you could find yourself faced with the latter thereby disproving the former.
If you are aware of the holes in airport security you should then acknowledge that you cannot keep determined, organized, and armed terrorists off the plane. A cockpit secured with a hardened door and protected by an armed pilot offers an increased ability to proactively deny the use of the aircraft as a WMD.
After 9/11 the temptation is too great for terrorism to resist trying to repeat that global attention getting feat again. Control of the cockpit is the focus and after all the airport security fails it is the secure and armed cockpit that keeps the plane from being used in this way again.