Tracking is one thing. Shooting down a civilian airplane loaded with passengers is quite another.
Prior to 9/11/2001, the doctrine was to wait out the hijackers, get the plane down safe and negotiate -- or storm the plane -- on the ground. It was the best approach to every hijacking to date.
You can argue from 20/20 hindsight that the planes should have been shot down, but the argument was equally valid that they should have been grounded before they ever took off. Or that Mohammed Atta should have been killed in kindergarten.
Everything is unprecedented the first time, and the 9/11 hijackers had the element of surprise. That tactic will not work again. It didn't even remain effective for one morning, once the Flight 93 passengers knew what was going on.