The nearly unbelievable level of rigor achieved by particle physics gives a harmful level of credence to numerous other fields, especially nutrition & medicine. Studies done across 8 people are given the same authorial credibility as studies done across 8 million protons, by lumping them all together as "science".
Yes, I think this has to be a major reason why people distrust science, and frankly I am sympathetic to it. Too many studies amount to a 2% statistical difference (with an analysis rife with biases) with no causal mechanism (or a highly speculative one). Relying on this type of evidence, while not worse than pseudoscience, still drastically weakens your position when trying to argue against claims like "vaccines cause autism". (Remember when fat was bad?) Also, even for the examples given in the piece, I think the truly "scientific" view has to be more nuanced:
- vaccines cause autism: OK, we have no reason to believe that they do, but we don't know for sure that nothing in them can cause autism. But even if they did, we believe the effect must be quite small.
- people are safer owning a gun: The science can't possibly say whether a particular person is safer or not owning a gun. But it does suggest that you may be underestimating the dangers of owning a gun.
- genetically modified crops are harmful: So far they have not really been harmful, but we have only a vague idea of the likely consequences down the road.
- climate change is not happening: Well, it's obviously happening, but a lot of similar questions are not clear. There's really no way to prove for sure that it's caused by humans or predict its consequences. We should still worry about it because of the potential consequences, but at the end of the day, we are still mostly working with educated guesses.
At the end of the day, even when science is wrong, I think it tends to give answers that are much closer to the truth than e.g. random intuition. So that's why some people arguing against pseudoscience try to paint the actual science as absolute truth. They're using the ends to justify the means. But their arguments are sometimes over-reaching, and that can ultimately make them lose credibility.