Who says it did?The whole point of a surprise attack.Your understanding is wrong. Have you ever been to Washington DC? If you had you would know the Pentagon is located right under the approach for Washington's Ronald Reagan airport. Any SAM battery would be shooting down airliners all day long!
My brother lived in Washington, D.C. for 3 years and I lived near NYC in NJ for 29 years. Unless you have lived in DC for a long time I probably know more about it than you do.
Here is the truth about missile protection for the Pentagon, not your guess:
http://www.wanttoknow.info/911/9-11_pentagon_missile_defense
You may remember that before 9/11, there were a number of tests of the Pentagon's missile defense systems. Some tests failed, while others succeeded. But there is an important question here. If these sophisticated military systems were designed to detect missiles fired from unknown locations at over 13,000 mph and shoot them down in mere minutes, why on 9/11 could they not detect any one of the four large airliners traveling at a mere 600 mph, especially when two of them were known to be lost for over 40 minutes before they crashed?
This question applies especially to Flight 77, which crashed into the Pentagon. The first plane hijacking on 9/11 was reported at about 8:20 AM (see NY Times article), well over an hour before Flight 77 crashed into the Pentagon at 9:38. According to the Times article, Flight 77 was reported lost at 8:56 A.M., 42 minutes before it crashed. Even if the FAA radar systems completely failed and FAA officials failed to alert the military, all military leaders certainly knew within minutes that the World Trade Center had been hit at 8:46. By 9:03, when the second tower was hit, they certainly knew there were big problems.
How is it possible that the Pentagon's highly touted missile detections systems could not locate Flight 77 in the 42 minutes it was known to be lost before it crashed into the heart of the defense system of the U.S.? The missile detection systems did not depend on FAA radar and were programmed to pick up any unaccounted for objects and raise alarms immediately, as mentioned on the CBO website.