The argument has to be approached logically, instead of with histrionics designed to evoke some emotional or contrived response.
First, the airlines would never be able to do this (from a legal standpoint) unless they required you to be "qualified" to carry the firearm. That means a training course and (at least) annual requalification. Besides which, if you're clever enough to operate an aircraft, I have to tell you, you're going to be able to "master" a firearm well enough to hit a target 3 feet away. It just isn't brain surgery. So the "what about the pilot who never fired a gun?" argument is moot.
Next, the object is to defend the cockpit so that the other pilot can immediately land the plane, not to go out and play "Diehard" with the hijackers. The passengers are the first line of defense (sad, but true), the (supposedly) armored door is the second, and the armed pilot is the last hope. Do you really want to NOT have that last line of defense? So the "shooting up the back end of the plane" argument is also moot.
Finally, as with virtually everything else on the plane, the final decision on whether or not to use deadly force will rest with the Captain. Given that there is probably now a fairly high percentage of captains who would intentionally destroy the aircraft rather than surrender control of it so it could be used as a bomb later, wouldn't you rather have another option before that "endgame" scenario?
Funny how folks whose careers revolve around doing something very technical in a very regulated, regimented, deliberate, precise manner, immediately jump to the conclusion that the concept of armed pilots would be implemented in some sort of haphazard, "cowboy" fashion, and that the same folks you trust to make hundreds of pretty important decisions each day couldn't be trusted to use that same degree of judgement regarding the use of a firearm in an "emergency situation."
Personally, I didn't have any desire to be armed in the cockpit in the military, and I don't have any desire to be armed now. That said, we all have to do things we'd rather not do, and if one of those things is to be in some kind of "combat situation" inflight, I'd just as soon not have to bring a fire extinguisher to a box-cutter fight.
At the very least, it would make those security checkpoint "discussions" a little more "interesting," eh? I doubt you'll get your ID card plucked off of your shirt when you're packin' heat
