The point that has been missed by who ever dreamt up this idea is that the terrorists on Sept 11 2001 had undergone many months of intensive training to complete their task. With a gun now being available in the cockpit all of the weak points mentioned by bogner and others will be investigated thoroughly by the terrorists and after many months of training they will gain access to a cockpit and will have a better knowledge and training to access the gun than the pilots themselves.
The pilots are now puting themselves in more danger as the terrorist will have to 'disable' the pilot much more quickly than before to prevent them getting to the gun before the terrorist does. This increases the likelyhood of a severely incapacitated (dead) pilot and no one at the controls, and a terrorist with a weapon which has been provided for him.