Let’s see…
First off, the average government isn’t going to be responsible for shooting down a plane with a few hundred people on it if they can help it. Ok, it’s been hijacked. Fine. We wait for them to *land*, hear what the hijacker’s demands are, etc. The concept of using a plane as a weapon really hadn’t been explored until 9/11. Sure, it was a problem, but it wasn’t a *threat*. Can you imagine what the uproar would have been if the planes had been shot down before they hit their targets?
Second: The planes actually didn’t deviate *that* far from the original flight path.. A quick hop of fifteen minutes, perhaps. By the time you can get a general on the phone, explain the situation, get the Go/No Go order, and get fighters scrambled, you’re not going to have much time to find the planes and shoot them down.
Third: The hijackers were trained well. They knew how to send the correct fake radio calls, etc, that made them appear legit. A plane that is off course isn’t going to be a major concern unless it’s veering into other airspace.
Now, granted, one of the planes *did* smack into the Pentagon, which arguably should have the tightest airspace int he country. However, having radar and fighter jets doesn’t promise a plane-free experience, as one russian pilot who landed in Red Square can attest..