Why doesn't he apparently trust pilots to be armed? Probably because he feels at this juncture that it is not politically expedient to do so. He's trying to maintain coalitions both domestically and internationally. On the domestic front, there are plenty of true believers in Victim Disarmament that would go ape-sh__ if he were to suggest that anyone other than the police/military carry arms on a routine basis.
For many, Victim Disarmament is a major part of their religion of state-worship. Attack this fundamental premise of their religion, that the state should not have a monopoly of lethal force and you'll see serious opposition begin to mount on many more fronts than we see now. I think that overall, he's being pragmatic in that he doesn't want to expend political capital (and being foolishly cautious IMO) by making such a suggestion. I'd like to see the pilots, cabin crew and passenger armed as well, but that is not going to happen in this country any time soon. Much more will be necessary to transpire before we regain our lost liberties.
I don't buy this. Americans are overwhelmingly for Pilots being armed. Where is the political risk, if in fact President Bush is serving Americans. Who would dare object, accept Bush.