The answer is that the people with their finger on the missile trigger knew the aircraft was no threat due to radar and visual interceptions and decided not to launch a dangerous missile into the middle of a huge city full of important officials since moving the President and other important officials to a basement would be sufficient to protect them from a Cessna. Instead, they waited for the plane to come down somewhere (on the lawn, it seems) and arrested the person inside.
> people with their finger on the missile trigger knew the aircraft was no threat due to radar and visual interceptions and decided not to launch a dangerous missile
I don't think we have evidence of this. The simple truth is the U.S. government doesn't fortify against domestic enemies in a systematic way.
> since moving the President and other important officials to a basement would be sufficient to protect them from a Cessna.
I think it's safe to assume that the bunkers under the White House are sufficient protection against as much explosives as a Cessna could possibly carry. The plane itself will do almost no damage, it's a flimsy thing built light out of aluminum and it's not even fast.
Not if you have ample time to move everyone to safety before it arrives. Seems a good trade off to make if you aren't confident what the pilot's intentions are instead of just blowing them out of the sky.