Pilots should definitely not be armed. Guns are very dangerous weapons and they do not belong on planes.
As a passenger, it does not make me feel more secure knowing the pilot is armed and dangerous, it actually makes me feel worse. The safety of the passengers should always be the number one concern, and arming pilots is very unsafe.
Armed pilots cannot prevent or stop a hijacking and/or terrorist attack, if anything they will make things more dangerous. The terrorist could easily disarm the pilot and take over the aircraft, or the pilot could go on a shooting spree.
Pilots should stick to flying the airplane, they should not be carrying guns.