Health bias — people who get vaccinated are already healthy, it only protects against the strain that it protects against but many strain of flu, colds and fly-like diseases can be flying about, all make the numbers used to justify the yearly push for flu shots and others vastly overstate their case:
But what if everything we think we know about fighting influenza is wrong? What if flu vaccines do not protect people from dying—particularly the elderly, who account for 90 percent of deaths from seasonal flu?
This position is being rebutted in various places. Some of their concern with the article is that is casts doubt on vaccines in pandemic situations, when the doubt is both misplaced (the vaccine is designed to be effective against the specific strain we are concerned about, and especially dangerous given its timing:
The bottom line is this. There is excellent and credible evidence in the scientific literature that vaccination against influenza reduces infections in people under 60, evidence that even Dr. Jefferson [the anti-vaccine guy: ed] of accepts. For those over 60, there are legitimate questions that were raised by others about the extent of the benefit of seasonal flu vaccine, but they were raised before Jefferson got into the act. The argument put forward in this piece is a straw man argument as far as pandemic influenza is concerned (and in which context it was placed).
Too complicated to summarize, but deeply worth reading both positions. It calls out the limits of knowledge and how easy it is to be led astray by experts as well as, similar to overthrow of our understanding of lactic acid, how deeply held beliefs could be completely wrong, or not. A statement that is true regardless of which side you come out on.