There are two forms such belief systems can take; evidence-based or faith-based.
Science is used to build an evidence-based belief system, under the premise that the world is ultimately understandable through observation, experiment, and prediction. The key element of science, is recognition that humans possess individual beliefs, and consequently are capable of introducing bias in their interpretation of the world. As a result, science attempts to mitigate against such bias by requiring strict definitions of terms and conditions, as well as demanding that any evidence be capable of independent verification by others. This ensures that accepted results have been subjected to trials that may also be subject to bias, but by strict adherence to procedure, such biases will cancel each other out and product conclusions that are largely objective.
Faith-based belief systems are mental constructs that lack evidence. This isn't to disparage them or to diminish their value, but rather to define an important difference. In short, a faith-based belief system is unequivocally based on the lack of evidence or evidence which may be impossible to collect.
Using these descriptions it is easy to consider faith-based beliefs as somehow lesser in value, but this would be incorrect. We tend to draw these conclusions, because regardless of what we individually believe, we are all convinced that our particular beliefs are the correct ones. It is this fascination with being "correct" that leads to such discrepancies. Therefore, we tend to defend our particular belief systems vigorously as being the only means by which one can experience "truth" or "reality".
However, it is important to note that not all beliefs are subject to verification and that this is precisely where these two forms of belief may often collide.
If we consider religion as a faith-based belief system, to many, science is viewed as demanding an atheistic perspective, but this is also incorrect, since science has nothing to say regarding such a belief. Science only requires that the world be explainable according to the "rules" that have been discovered regarding its behavior. Therefore, any postulate that suggests something that operates outside those rules is uniformly rejected as being unscientific.
One cannot introduce faith into an evidence-based system any more than one can demand evidence of a faith-based system.
We see a similar conflict in conspiracy theories which are also faith-based systems. While these are often disparaged as the product of mental defectives, it is useful to examine the basis by which such beliefs are generated. In this case, they attempt to straddle the line between evidence and faith, but manage to construct rules of evidence which can never be satisfied. This becomes self-reinforcing to continue bolstering the conspiracy, since any explanation must, by definition, be part of the conspiracy which hides the information desired.
From these we can see that people are capable of constructing all manner of individual beliefs by which they tell stories about how the world works. Some may argue that science is as much subject to faith as religion, but this misses the larger point. Admittedly, scientists will accept others research results "on faith" because the underlying premise, that is shared in science, is that it will be (or has been) verified by others and therefore warrants inclusion in a worldview that is explainable by evidence.
In cases, where the data is inconclusive, then opinions may vary and controversies ensue, but invariably these results will eventually be settled as more evidence is examined.
Faith-based belief systems are invariably solely subject to interpretation. Opinions are never resolved except by consensus. If enough individuals agree, then a particular tenet of belief may be solidified, but it is never truly subject to challenge because there is never any expectation of evidence to consider.
In the case of our conspiracy theorist, the evidence is simply precluded from consideration, because the provider of such evidence will always be suspect as being a party to the conspiracy itself. Since verification becomes impossible, the construct of the conspiracy holds. What is interesting in this case, is that even disagreement among conspiracy theorists tends to support their claims, because the challenge isn't about any particular event. The issue is the lack of "openness" in accessing the data. As a result, it is irrelevant when conspiracy theories exist that are contradictory, since that may even be expected. After all, the conspiracy is the lack of access to data; not the event itself.
As humans, we tend to use all these belief systems to varying degrees to cope with events in our lives. Ultimately we need the world to make sense at some level. Therefore, those areas where that "sense of reality" is most challenged will tend to be the areas in which the most controversies exist. We can tolerate all manner of rules, but we can't tolerate the idea that the world operates according to no particular rules. Concepts like "randomness" drive us crazy. We expect a purpose and a meaning. Therefore, we are inclined to reject any idea that suggests that there is no purpose or meaning.
Therefore, when science ventures into areas where such ideas dominate, they will tend to be the most contested topics. It isn't that scientists are better equipped to deal with uncertainty. It's just that scientists have collected more evidence and data, which allows them to make sense of the "randomness". The world still has purpose and meaning. It is simply different.
Similarly, our conspiracy theorists, want to claim a worldview in which events don't happen without reason. Instead, they want to create a scenario in which all events are linked to a higher manipulating power. Lee Harvey Oswald, can't simply have a lucky shot. He has to be an expert marksman. The 9/11 terrorists weren't simply lucky in their execution of their plans. They had to have assistance from higher powers and secret agencies. Everything is the result of a carefully orchestrated event for which we will never be able to gather the necessary data to expose the conspiracy.
We find the same tendency in many religious beliefs, where bad things happen because of the result of demons or Satan or some source of evil. This is opposed by the forces of good, which will ultimately have a major confrontation in which the forces of evil are forever defeated. In each instance, we want to presume that events have a purpose and that they have been executed by someone with intent.
It is simply intolerable, to most, to consider that bad things can happen for no good reason and that good doesn't always triumph. The world isn't a hostile place. It is indifferent. So, we construct our respective belief systems so that we can tell the stories that make us feel most comfortable. In that world, everything always has a reason.