During the Cold War, there was a good deal of resources devoted to US airspace defense, especially back in the 1950s before the missile era. We had many interceptor squadrons on alert around the country, the Distant Early Warning (DEW) line of radars looking outward for inbound bombers, and C2 (command and control) centers watching over everything.

All of that changed beginning in the early 1960s. The Soviets never built a large force of intercontential bombers. Instead, they built up their long range missile forces. Many of the 1950s era interceptor squadrons were deactivated and many others were transferred to the Reserves. With the end of the Cold War, the interceptor forces were cut even more.

The guiding assumption all along was to look out for inbound planes from outside our borders. No one seriously considered even a single hijacked airliner being used as a suicide weapon, much less four of them at once. When the hijackers took over the planes, one of the first things they did was turn off the transponders which made them even harder to track. There were over 4000 airplanes airborne nationwide, so identifying the four planes that were off of their flight plans wasn't a trivial job. The result was that there wasn't enough time to get the few remaining alert interceptors airborne in time to intercept the planes.

In retrospect, it's easy to see the missed intelligence signals that hinted to the attacks. However, hindsight is always 20-20 (barring historical revisionism). In retrospect, it was obvious that the Japanese were going to bomb Pearl Harbor, too. (And no, I'm not a conspiracy buff who thinks FDR knew the attack was coming but did nothing so we would be forced into the war). However, military operations happen in realtime, not in retrospect. When you're one of the intelligence analysts trying to sift through 2 million communications intercepts per hour or an Air Traffic Controller or NORAD crewmember trying to oversee countless planes to see if any of them are misbehaving, its rather hard to manage the sheer volume of information, much less to anticipate what might happen.