If by "they" you mean the U.S. military, the answer is that they were unprepared to deal with the use of hijacked commercial jets being used as missiles, and did not have time to sufficiently react to the situation before it was over.
Unprepared? Yeah, sure.
One part of Operation Bojinka was the crashing of a hijacked airliner into CIA Headquarters at Langley, Virginia.
So, for more than five years, the military was aware of terrorist plans to use hijacked airliners as missles. There was simply no excuse for being unprepared on Sept. 11th, 2001.
Of course, I know that my rational answer will never suffice for the OCT defender.