"I don't believe that anyone in the military would shot down a passenger airline (excepted one controlled by terrorist). And if they believed that is what they were doing, they would not keep it a secret."
I happened to be an observer a few years ago when two Navy missiles were fired from Wallops Island for the purpose of hitting a drone off the east coast of the U.S. Perhaps flight 800 was in the wrong place at the right time. That would explain the presence of other military assets in the area that night.
If there were a missile test for the purpose of testing SDI technology for example, you can be assured that it would be classified so highly no one would talk about it.
I'm not saying I believe that's what happened (I tend to believe it was a terrorist hit), but that is a plausible explanation as to how the military could have been involved.