On the subject of freedom of religion, Thomas Jefferson once said "But it does me no injury for my neighbor to say there are twenty gods or no God. It neither picks my pocket nor breaks my leg."
I've always thought that was a pretty good quote--that it more or less summarized what the Libertarian view *ought* to be. People should be free to do what they wish, so long as it neither breaks my back nor picks my pocket. But the fact is, the people who call themselves Libertarians these days are generally whiny self-entitled jerks who don't seem to have any understanding larger than themselves. Basically, they're still stuck with the same petulant mentality the rest of us had as teenagers, but thankfully grew out of.
Under that Jeffersonian maxim, your rights end when your actions have consequences for other people. When you don't get vaccinated, you put yourself at risk. Just like driving without a seat-belt. So far, no problems. But you also put other people at risk. Organ transplant recipients and AIDS patients who are immunosuppressed and people with allergies (usually egg allergies) who can't get vaccinated depend on the herd immunity provided by having the rest of us vaccinated. As long as everyone else is immune, there's no one to spread diseases to them.
If you choose not to vaccinate yourself or your child, you don't just put yourself or your child at risk, you put all those other people at risk too. It's only a small amount of risk, but in the aggregate it matters. It's just like driving drunk--everyone else on the road is a little less safe because of your actions. Maybe it'll amount to nothing, but those risks weren't yours to take. You don't have that right and it's the governments job, on behalf of the rest of us, to make damn sure you know it.