Airplanes only represent a unique terror target if they can be used as weapons to inflict greater damage. Putting a bomb on a plane will kill several hundred people, but so will putting a bomb in a mall or train.
Thus, securing the cockpit gets you more bang for the buck by removing a whole avenue of attack, with relatively low cost (the lock and the gun). While I agree that firing a gun in a pressurized cabin isn't the best idea, having it there makes it very likely that the pilots would have an advantage over any potential hijacker, since keeping other guns off the plane is relatively easy, and doesn't require overly invasive searching.
Thus, securing the cockpit gets you more bang for the buck by removing a whole avenue of attack, with relatively low cost (the lock and the gun). While I agree that firing a gun in a pressurized cabin isn't the best idea, having it there makes it very likely that the pilots would have an advantage over any potential hijacker, since keeping other guns off the plane is relatively easy, and doesn't require overly invasive searching.