Having said that, I'll mention a couple of things that need to be addressed before I will ever be convinced that this was not a shoot-down:
1. Why the fraudulent testing by the NTSB?
2. Why the idiotic animated re-construction of the incident, showing the aircraft climbing a few thousand feet even after everything from the wings forward had been blown off?
3. Why the secrecy about what the Navy was doing in the area that night?
4. Regardless of the discrepancies between the various eyewitness accounts, you simply cannot discount the number of people from a wide range of points along the south shore of Long Island who saw something (or things) resembling a missile climbing through the sky that evening.
5. Why were the FBI and CIA involved in the investigation from Day 1? This was the first indication that something was highly unusual about this incident -- the FBI and CIA do not get involved in "ordinary" airline disasters.
I don't understand why you cannot accept the notion of the U.S. Navy shooting down a civilian aircraft -- it's not as if it hasn't happened before.