The hijackers on 9/11 took advantage of a window of opportunity that was only available up until 09:37 on Tuesday September 11th 2001 (the moment the Pentagon was hit). From then on it was apparent to the passengers on United Flight 93 and the rest of the entire world that the classic hijack scenario had ended and the tactics had now radically changed.
No aircraft that has been hijacked since will have its passengers meekly sit subserviently as they fly to their doom. Likewise air forces on the ground will prevent any aircraft getting near built up areas.
It is also highly probable that had the US Government actually been paying attention to the threat posed (they had numerous warnings from Mossad and German intelligence amongst others) and the CIA and FBI had been sharing their information, they would have apprehended Atta and the others before they got anywhere near commercial aircraft that morning.