Relying solely upon common fucking sense (I don't have time to write a term paper on the subject) I'd say vaccinations are still way more helpful than they are harmful otherwise they wouldn't be offered anymore. Once Science proves otherwise I'm sure policy will change accordingly.
With that said I don't think the government should be able to FORCE anyone to inject anything into their bodies, however, if you want to be a part of any government institution (public schools, military) or government regulated institution (such as daycare) then I think they should have to abide by the rules including vaccinations.
Home schooled kids in rural living situations would be one of the lone exceptions as long as they aren't getting any kind of government assistance INCLUDING government subsidized healthcare. You aren't going to NOT get vaccinated, then get sick, and then expect my taxes to pay for your healthcare.
In other words I'm fine if people want to be stupid in a vacuum as long as it doesn't have any chance to effect others.