The F-16s at Andrews are National Guard, not active duty AF. The primary mission of the active duty forces at the base is Airlift and transporting the President and his entourage, not air defense.
Just because a base has some fighters assigned doesn't mean that the mission of the base is defending nearby cities and national monuments from air attack.
Prior to 9/11 the air defense focused on Communist bombers that routinely fly down the coast of the US to Cuba and the detecting and countering cruise missiles, not shooting down passenger jets.
And as I have tried to tell some folks, just because it has fighters assigned, doesn't mean they're sitting around hot cocked and ready to rock (as we called it when they were sitting alert duty)