If Flight 93 had exploded in the air...
then debris would've been spread over a wide area as it was with the Pan Am 747 destroyed over Scotland by a terrorist bomb. Instead, Flight 93's debris was in one small hole, indicating that it impacted the ground intact at very high speed, possibly nearly straight down. Accident investigators have decades of experience at determining the cause of a crash. They can even tell if a light bulb was lit at impact from the reminents of the filament. It isn't hard to recognize the signs of a plane being shot down. Flight 93 had none of those signs.
That said, there was a fighter being scrambled to intercept Flight 93 and shoot it down if necessary. Flight 93 crashed over 10 minutes before the fighter was anywhere near it.