Guns vs Other Stuff Tapped makes a silly argument against pilots carrying guns in the cockpit.
"Sure, it's dumb. If you have to get into a firefight in the air to stop a highjacking -- that is, if terrorists already got their weapons aboard -- you're pretty much already screwed."
Sure, an onboard gunfight could be nasty, but I suspect guns would be fairly effective against, say, boxcutters.