Over at Rationalist Judaism, the discussion has come up regarding vaccination and R' Shmuel Kaminetsky's support for parents who choose not to vaccinate their children. There is much to be said about this topic, but I don't have much to add that hasn't already been said. The most comprehensive and rational treatment I've seen yet is R' Asher Bush's article in the Hakirah Journal here. Another nice article, which gives a little bit of a historical perspective as well, is by Dr Eddie Reichman in Jewish Action here.
Frankly, I am not sure what to make of this trend or how to approach it. It is clear that the objection to vaccination among the "non-vaccinators" comes from a deep-seated mistrust of modern medicine. This can be prevalent among Chareidim, which is probably mostly a result of the overall mistrust of science that is so ingrained in that society. However, it is also common among many other groups, such as the growing number of liberal minded people who are mistrustful of the medical establishment, which they consider part of the corporate, profit-oriented elite.
When these two forces are allied, it is impossible to overcome the prejudices that are inevitably the key factor in forming opinions on this matter. It is hard enough to convince a non-religious oponent of vaccination by presenting the medical evidence that contradicts his/her views. They will always claim that it was cooked up by the pharmaceutical companies in order to make a profit selling vaccines. However, it is exponentially more difficult when the belief in that conspiracy theory is compounded by a belief that all science is only relevant if it is approved by "Da'as Torah."
I honestly have no idea how to overcome this problem, and I am very afraid that it will be getting worse and worse in the coming years. At least the readers of this blog should inform themselves about vaccinations, and a great start would be to read the articles I linked to in the beginning of this post. I don't think I have much more to add. Shabbat Shalom.