Let me start by reiterating that freedom is, for me, the primary purpose of law and government. As I've argued many times on this blog, laws constraining our freedom are justifiable only if they lead to a net increase in our practical freedom. So freedom is really important to me.
That said, there's a certain kind of appeal to freedom argument that is just total nonsense, because there are some circumstances where alternatives are simply incompatible, where my exercising my freedom of choice makes it impossible for you to exercise yours. The best example of this is the complaint of smokers that their freedom to choose to smoke or not to smoke is violated by the imposition of anti-smoking bylaws to public spaces.
On the face of it, yeah, it's absolutely true that such rules take away the freedom to choose to smoke in such public spaces. What's not quite so immediately obvious is that, owing to the nature of smoke and air, there is an enormous disparity in the power of smokers and nonsmokers to exercise choice. The choice not to smoke must be unanimous, whereas any single smoker may unilaterally decide that they and everyone else in that space will inhale smoke.
I want to go to eat in a restaurant without smoking. You want to go eat in the same restaurant and smoke. We can't both get what we want. Someone's options are going to be limited here, no matter what policy we choose. Allow smoking, and I can't go to a restaurant without giving up my freedom to breathe fresh air. Disallow smoking, and you can't go to a restaurant without giving up your freedom to light up a cigarette. Flag-waving about freedom is pointless; what you need to show is that your freedom to smoke is somehow more valuable than my freedom not to smoke. (This particular question has been mostly resolved by the widespread acknowledgment that smoking really does cause cancer and other diseases.)
Although complicated by the fact that you can't see or smell viruses, the situation with vaccine mandates and various public health measures is analogous. I hear people complain that they can't go to church or to a restaurant or anything else without showing their vaccine passport. Oh no. Well, the alternative is that I can't go to these things without taking on a major risk of being infected with a deadly virus. Someone's options are going to be limited, one way or the other; we can't all get what we want. So whose options should we limit?
I don't mean to answer that question here. There are an awful lot of factors involved, and an awful lot of different pandemic measures we could debate. Some may turn out to be good ideas, some may be bad. The only point I want to make here is that freedom can be violated in a whole lot of ways besides just imposing an explicit rule, and if we really want to maximize our freedom, we need to think about more than just whether or not someone is telling us what to do. Viruses can take away your choices, too.