The text of the final Airport Security bill has been released.  Pilots can be armed, sort of, only if those in powers over them give them permission and approve their firearm.

SEC. 128. FLIGHT DECK SECURITY.

The pilot of a passenger aircraft operated by an air carrier in air transportation or intrastate air transportation is authorized to carry a firearm into the cockpit if--                                          
(1) the Under Secretary of Transportation for Security approves;      

(2) the air carrier approves

(3) the firearm is approved by the Under Secretary; and

(4) the pilot has received proper training for the use of the firearm, as determined by the Under Secretary.