I appreciate civil liberties more than the next guy, perhaps because I'm a libertarian and not an anarchist. What do we mean when we say we're free? Anarchists will say our freedom is "inherent" but this can't be right because freedom only means something in the context of having to live with other people. Where does your freedom end and mine begin?
We can only answer that question when we reach some agreement about what behaviors we're tolerate and protect. And we're obligated to protect each others' freedom, so freedom comes with responsibility. If I don't pay my taxes, I'll be sent to jail. If I don't fight for the country if I'm drafted to, I'll be sent to jail. If I resist being sent to jail, I'll be killed.
Now, I think our taxes are way too high and the government through which we establish and protect our freedom fights too much and imposes way too many restrictions on us. Mostly I think they're fucking idiots. But I'm obliged to these idiots nonetheless because the relative health, prosperity and freedom I enjoy is premised on us being responsible citizens and meeting the trivial responsibilities we have to each other.
The vaccination responsibility is trivial. I'm not asked to go to war. I'm not asked to believe in any particular religion. I'm just asked to take a couple seconds of minor pain and a trivial risk that I'm one of the 1 in 1,000,000 people who actually have a bad reaction. It's irrational to worry about this. Even with improved hygiene, thousands, probably tens of thousands would get sick and die without vaccines every year. The cost benefit to vaccines isn't worth talking about.. It'd be much more rational to complain that you're being taxed too much for shitty schools, worthless politician, enfeebling social programs, crony capitalism and needless wars.
Taking away my ability to provide for my family is a much greater obligation than getting a shot, and I think folks are giving in to baseless fear to put one in front of the other.