It isn't a dumb question at all; in fact, it goes to the heart of the problem of how conspiracist thinking is fundamentally broken. There was a post here a while back - and I'm sorry, but I forget who it was - that summed up the problem: while most people categorise facts into which hypothesis they support, conspiracy theorists categorise facts according to whether they agree or disagree with the conventional understanding of events. They then make the mistake of thinking that any facts disagreeing with this understanding are necessarily supportive of their conspiracy theory. A good example is that truthers see a minor disagreement between different analyses of the WTC collapses, some of which argue that the fires alone were sufficient to cause collapse while others argue that the impact damage was also a major factor, and claim that this debate is evidence that no combination of fire and impact damage could have caused the collapse. However, since they never state their beliefs this clearly, it takes a little time to tease out the fact that that's what they actually mean, by which time they've given the impression of having a valid argument.
The Flight 93 shoot-down theory is a fine example of this broken thinking. The official story is that Flight 93 was deliberately crashed by the hijackers to prevent the passengers gaining control, therefore anything that suggests any other possible interpretation is seized on by a conspiracy theorist as proof of their own conspiracy theory, even if it directly contradicts it.
Beyond that, it's probably best not to look for rational analysis from the truthers. A movement whose leader has claimed its lack of a coherent hypothesis as one of its greatest strengths is hardly the best place to find any coherent reasoning.
Dave