I can't say for certain, but I suspect self-deception on the part of many of the witnesses. Unless they sequestered themselves immediately, and wrote down their impressions, they're vulnerable to re-interpreting what they saw in light of further news/conversations, and even re-thinking the event. And it was a horrific event that would obviously be etched in their minds. Rush recently mentioned a study that showed how a large portion of test subjects were easily convinced that they remembered Daffy Duck at Disneyland when they were kids.
A shoulder-fired SAM is a tiny missile, with a small flame, and a thin column of white smoke. Depending on how far the witnesses were from the probable launch site, it might be too faint to really be seen. Also, why were these people looking at that spot in the sky anyway? The plane itself was unremarkable.
It would take at least 15 seconds for even a supersonic SAM to reach that altitude. How many people were watching that entire time? And if they weren't watching from the start, what caused them to switch to the scene? My own theory is that they saw the breakup and explosion of the main explosion of the plane, which was shooting upwards, trailing fire and debris. The human mind then provides the "reasonable" explanation, a fire trail from the ground to what they saw in the sky.
I'm not saying these people lied, but there are plenty of opportunities here for honest self-deception. From what I've read about missile hits, only a powerful bomb placed at the right location in the aircraft structure could produce the type of damaged indicated.
It would be bad enough for 800 to be taken down with a SAM. But even worse if a bomb, produced and placed by someone with expert knowledge, was the real culprit. The klinton regime quickly decided that campaign contributions from the airline industry was far more preferable than telling the American people that we were under terrorist attack. So they produced the "center fuel tank" myth, that merely stated that every 747 has always been a potential flying bomb.