Ok, but I think you're missing the point here.
It would be OK if you were to refuse vaccinations and only you had to bear the costs of that decision: You get sick, you die, the end.
That is not the case here. There are, potentially, huge external costs to your decision. You may get sick and infect others with poor immune systems. Other people might die.
I think a good comparison here would be parents who expose their children to second hand smoke. Sure, it's your choice to smoke, and if you get sick or die from smoking, fine. But when you force others to bear the consequences of your decisions, and impact their health, well, that isn't fair and it shouldn't be legal to do so.
EDIT:
First, most of these parents are not making this decision for religious reasons any more than they are not eating gluten for religious reasons.
Additionally, hiding behind religious expression/freedom is BS. There are plenty of religious practices that would be illegal if followed. I know it's cool to be PC, but you need to stop somewhere. If a religion promoted cannibalism or human sacrifice, we certainly wouldn't allow that, would we?