Reinforced doors and a belief among everyone from passengers to pilots that a successful hijacking is likely to lead to death rather than inconvenience reduced hijacking after 2001. I would be surprised if searching passengers more aggressively or requiring people to prove their address to get a driver's license had much to do with it.
Yeah, I think passenger game-theory is the number one reason, and that was already in place on September 12th, 2001.
Passengers are now aware that hijackers might actually just buying time until they can trigger a murder-suicide attempt, and many will believe it is likely enough that they need to fight for their own lives. The old assumptions that "almost everyone gets out alive by passively cooperating" no longer hold.
Who's we? Al Qaeda reduced it down to ~4 per year because now passengers no longer assume to survive and act accordingly. Locked doors and plain clothes security are just icing on the cake.
Look at all those other pre-2001 hijackings, and ask yourself what would have happened if most of the passengers were terrified that the hijackers were preparing to destroy the entire plane and everyone on it, regardless of any demands being made or met.
Would-be hostage-taking hijackers know it too: Their business plan, as it were, has been ruined for a generation by their suicidal colleagues.
Airline and security protocols are no longer "comply with everything so that nobody gets killed". Doors are locked. Passengers will likely bum rush you. There might be armed security on any given flight. The odds of success are unbelievably long compared to what they were in the 80s. Just not worth it vs a "boring" bombing or whatever.