If someone had a gun on September 11, 2001 perhaps the history would be different.
Pre-911 being hijacked meant "If you sit down and be quiet, we fly this plane to Cuba, protest for a bit and then everyone goes free. An inconvenience, but nobody gets hurt. If you try to fight back, you'll be killed." So even if someone had a gun in the first two planes, they would have likely kept quiet until it was too late.
The passengers in the third plane did try to shoot back when they found out what happened to the first two planes, but a passenger with a gun might not have made much of a difference. At that point, the terrorists had control of the airplane and even a gun wouldn't have given the passengers the upper hand quick enough to keep the terrorists from crashing the plane.
Nowadays, if someone tries to hijack a plane - even if they intend the "flight to Cuba" kind of hijacking - the passengers are going to rise up, guns or no guns.