For me, one of the most important issues in this balance is who bears the risks? If I and my children are vaccinated, then the risks of not getting vaccinated are borne primarily by those who choose not to get vaccinated. If that's the case, I would tend to err on the libertarian side of things.
If there are instances when the general public is at risk because of a large unvaccinated population, then the case for universal vaccination becomes much stronger. For example, if my infant child is likely to die of measles because too many older children have gone unvaccinated, that may be a compelling reason to require most school age children to be vaccinated.
Personally, I think most vaccines are worthwhile but there are exceptions. The chicken pox vaccine prevents a disease that usually isn't very serious when contracted in childhood, but it wears off and you can then contract chicken pox later in life when it is more painful and can potentially result in infertility.