It's an interesting question. I do think a lot of people who claim to be 'questioning the science' are doing so with some kind of background agenda. The trouble is, there can be a lot of data, and it's not realistic for a layperson to keep on top of it all.
There can also be genuine disagreement between genuine scientists about what the data shows. In issues such as virus transmission, there are a lot of variables that are hard to control for.
I remember when mad cow disease appeared. I was working at a University at the time, and interacted with some people who worked in diseases. I was worried about inter-species transmission -- he told me that, though it wasn't his area of specialty, he had just been to a talk by one of the experts who had assured the audience that it was absolutely impossible for this kind of disease to jump across species. And that he had no concerns about letting his children eat mince.
I admit that, on purely philosophical grounds, I was then just too worried that not enough was really known about this disease and, personally, kept away from mince.
A year later, they had discovered a new mechanism of transmission hitherto unknown, via prions. When I met the scientist again, he admitted that the new theory changed everything and that he no longer let his family eat beef!
Note this though: he was completely open about changing his mind in the light of new evidence. And, though I turned out to be right to be cautious, I don't think I knew better than the scientists.
Overall, I think we should be allowed to question the science but whereas I was in the privileged position of being able to interact with honest researchers, I think today there's a lot of bad faith in the way that the science is presented I think if the scientists were allowed to speak and people engaged their minds with what they said, we'd have an all-round healthier society.
With facebook, youtube, and these strange internet echo chambers, I don't see that happening any time soon.