1. Flight 800 was flying lower than usual through the area that night. It had been ordered to reduce its altitude to make way for a northbound flight into Providence, Rhode Island that was running behind schedule. A terrorist would not possibly have known this advance, when selecting a location to shoot it down.
2. The U.S. government, after months (if not years) of stalling and prevaricating about it, finally admitted that there were naval assets deployed in the area south of Long Island that night to conduct military exercises. The lack of any obvious reaction from these ships (I believe there is documented evidence that they all vacated the area that very night) would run counter to any reasonable reaction to a nearby terrorist attack using a surface-to-air missile -- in other words, the proverbial "dog that didn't bark" scenario.