Armed pilots is a dumb idea. You'd do better to secure the cabin door, and hey-ho that's what they've done. Giving pilots weapons is just going to make them think that they can use them to defeat the hijackers, and they'll open the cockpit door, which is exactly what the hijackers want you do to.

Is it? I'm pretty sure the cabin door flying open unexpectedly and a stream of hot lead coming out is exactly what a boxcutter-armed shahid DOESN'T want. Unarmed pilots have no choice but to cower behind the locked door until it eventually gets cracked open... most likely by a co-pilot who got a knife put at his/her throat while taking a pee break.

Armed pilots AND a locked door, on the other hand, multiplies the hazard level to the jihadis. They might stay behind it until they land and a SWAT team takes the terrorists out, or they might pop the door open, kill one or more of the hajjis, and lock it up again. The ultimate defense is one that transfers the elements of surprise and initiative from the attackers to the defenders, and neither just arming the pilots (who could be jumped and killed while distracted by their plane-flying duties) nor just reinforcing the cabin door (which the pilots would routinely have to leave the safety of) would do this.

Of course, having Barney Fife for your pilot makes pretty much any preparations pointless, since he's likely to shoot himself and his co-pilot in the foot and then throw his still-loaded gun at the terrorists.