Some people have an irrational and delusional distrust of vaccination. Yes,it's true: some vaccinations can have side effects that are, on rare occasions, serious. But, generally, the malady is far worse than the cure.
One of the reasons some people distrust vaccinations is a man called Andrew Wakefield. He claimed that there was a link between (the administration of) the measles, mumps and rubella (MMR) vaccine, and the appearance of autism and bowel disease. His fallacious hypothesis led to a drastic drop in vaccination coverage in the UK and other countries, with a consequent increase in the incidence of measlesand its complications. His paper was so willingly riddled with fraudulent data (the commission found three dozen charges proved, including four counts of dishonesty and 12 counts involving the abuse of developmentally challenged children) that it has eventually been retracted by the editors of The Lancet and Wakefield was struck off the Medical Register in May 2010. He can never work as a doctor again.
More trustworthy research has not been able to find one shred of evidence that vaccination causes autism (or any other illness or disorder). Still, some people continue to see Wakefield as a sort of martyr and they still maintain that the MMR vaccine must cause autism. Why do people rather believe someone who’s a known fraud and not trust honest science?
quackery and your brain must know it on a certain rational level, but you explain it away because you want to believe it works.
As a result people put their children in potentially mortal danger by refusing to give them their vaccinations, because they think the tiny bodies of infants are being overwhelmed with too many antigens. However, the antigens in the vaccine schedule has actually decreased over the years (as the vaccines have become more targeted), and the number of antigens children face on a daily basis from the environment vastly outnumber the few additional antigens in vaccines. Which resulted in a surge in pertusis cases in the USA.
Even the annual flu-shot is distrusted because some (still) contain Thimerosal, a mercury-containing organic preservative. The reasoning for the Anti-Vaxxers is simple: mercury is a poisonous substance and therefore the flu-shot is specifically aimed at killing you. The FDA have extensively tested Thimerosal and decided it was safe to use at levels far higher than are used these days in vaccines. Most Influenza vaccines do not even contain Thiromersal.
BTW: The Human Papillomavirus (HPV) vaccine was given to Australian girls since 2007 and researchers now found that the rate of genital warts in young Australian women decreased by 61 percent, while rates in age and sex groups not covered by the program were unchanged. See here.
 Wakefield et al: Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children in The Lancet - 1998
 Kahn et al: Case-control study of vaccination history in relation to pertussis risk during an outbreak among school students in The Pediatric Infectious Disease Journal - 2006
[3 FDA: Thimerosal in Vaccines. See here.