9/11 was different. People cooperated because that was protocol at the time for a plane hijacking. Nobody expected them to use the plane as a weapon with no regard to their own lives. This was an unprecedented attack.

http://en.wikipedia.org/wiki/Aircraft_hijacking

"Before the September 11, 2001 attacks, most hijackings involved the plane landing at a certain destination, followed by the hijackers making negotiable demands. Pilots and flight attendants were trained to adopt the "Common Strategy" tactic, which was approved by the FAA. It taught crew members to comply with the hijackers' demands, get the plane to land safely and then let the security forces handle the situation. Crew members advised passengers to sit quietly in order to increase their chances of survival. They were also trained not to make any 'heroic' moves that could endanger themselves or other people. The FAA realized that the longer a hijacking persisted, the more likely it would end peacefully with the hijackers reaching their goal.[12] The September 11 attacks presented an unprecedented threat because it involved suicide hijackers who could fly an aircraft and use it to delibrately crash the airplane into buildings for the sole purpose to cause massive casualties with no warning, no demands or negotiations, and no regard for human life. The "Common Strategy" approach was not designed to handle suicide hijackings, and the hijackers were able to exploit a weakness in the civil aviation security system. Since then, the "Common Strategy" policy in the USA and the rest of the world to deal with airplane hijackings has no longer been used."

There was also a change in protocol after the Columbine High School massacre. In that attack the two were able to shoot victims while the police were outside setting up a perimeter. Now as a direct result of that attack police actively charge an active shooter, this is called Immediate Action Rapid Deployment. This is said to have saved dozens of lives in Virgina Tech alone.