In my experience, if there is a field where there is a big consensus opinion among "experts", and a small group of wacko's on the internet contesting the "expert's" finding with their own citations to the scientific literature, if I've investigated and read what the science says, the wacko's have turned out right every time
And other than vaccines what are your issues where you think this? Also, what makes you think that this is actually what is going on and you aren't falling prey to a basic desire to be special and have access to the truth?
Vaccination is probably one of the hardest topics to have a rational discussion about. I have some reason to believe that the author of http://whyarethingsthisway.com/2014/10/23/the-cdc-and-cargo-cult-science/ is someone interested in looking for the truth, not winning a side - at the very least, I'd like to help him when he says this:
I'm getting started on reading the actual papers, but I'm hoping this finds someone who's already done the work and wants to go post it on his site, or if not, someone else who's interested in looking through papers with me - I do better at this kind of work with social support.