I have mixed feelings on this as well. I have a lot of libertarian friends who are adamantly opposed to vaccinations. My dad is a doctor, so my perspective on it is quite a bit different than theirs. Most of their issues with vaccinations are the unproven and unsubstantiated claims that vaccinations can cause certain disorders (especially in children). I think most of that is nonsense.
I have a lot of libertarian leanings, and I would certainly support and love to see more libertarians elected to office. I would easily trade off the alternatives with libertarians even when they're wrong. HOWEVER, strictly speaking, I am not a strict libertarian. I don't even technically consider myself a libertarian -- I'm a pelocon but that is awfully close on most issues.
I believe it's very very important to get a vaccination. Whether the state should force someone to get a vaccination is another matter, but I lean slightly in favor of it. It is a public health issue, but on the other hand the only people who would be affected by not having a vaccination are the people who chose not to get a vaccination therefore it's their fault if they wind up sick and die.