The difference with Flight 800 is that those who disbelieve are not all people who believe in the bizarre counter theories. Some of those who doubt -- simply doubt.
Interesting logic.
This is one good way to refute the tinfoil crowd. The Muslim pilot's voice on the black box recorder chanting, "Allah Akbar Allah Akbar Allah Akbar..." as he slammed that jet into the ocean floor.
http://www.emergency.com/1999/egyp990.htm
That's one difference.
Another difference is that with 9/11 conspiracy theories you have to explain away the 4 airplanes that were hijacked that day. There is no such hurdle with Flight 800.
Another difference is what witnesses saw. On 9/11, lots of witnesses saw planes fly into the World Trade Center and the pentagon. With Flight 800, lots of people saw something that saw looked like a missile hit the plane. Thus with 9/11 eyewitnesses tend to support the official version, and with Flight 800 eyewitnesses tend to support the conspiracy theory.