One potential explanation is needle phobia, and people invent rationalizations on top of this. I don't find it prima facie implausible that people strongly dislike violations of their bodily autonomy. This is, after all, the reason why we have laws against non-consensual touching and sexual assault.
This theory has the advantage that it explains why people seem less skeptical of government coercion for other things. My sense is also that I find relatively little resistance to the idea that we should take emergency-approved medication if we're hospitalized with COVID-19.
Wikipedia states,
It is estimated that at least 10% of American adults have a fear of needles, and it is likely that the actual number is larger, as the most severe cases are never documented due to the tendency of the sufferer to avoid all medical treatment. The diagnosis criteria for BII phobias are stricter, with an estimated 3-4% prevalence in the general population, and this also includes blood-related phobias.
Prevalence of fear of needles has been increasing, with two studies showing an increase among children from 25% in 1995 to 65% in 2012 (for those born after 1999). Augusta University professor Amy Baxter attributes this increase to an increase in administration of booster shots around the age of 5, which is old enough to remember and young enough to be more likely to result in formation of a phobia.
As for myself, I find it somewhat disturbing to be stabbed with a needle. I can cope with vaccines, but in the few instances in my life in which I needed to draw blood, or have a drug administered intravenously, I remember feeling extremely queasy. It's overall not a fun time.
I'm not sure, but it's clear that some cultures have more collectivist norms, which translates into more social pressure for people to get the shot, even if they don't like it privately.
I’ve been fairly confused by the popularity in the US of remaining unvaccinated, in the face of seemingly a non-negligible, relatively immediate personal chance of death or intense illness. And due to the bubbliness of society, I don’t actually seem to know unvaccinated people to ask about it. So in the recent covid survey I ran, I asked people who hadn’t had covid (and thus for whom I didn’t have more pressing questions) whether they were vaccinated, and if not why not. (Note though that these people are 20-40 years old, so not at huge risk of death.)
Their responses:
The biggest themes mentioned here seem to be distrust or hostility regarding the government and media and their various pro-vaccination pressurings, and the impression that the vaccine doesn’t work. (I wonder how much that one is relative to an expectation of ‘very occasional breakthrough cases’ that one might also trace to someone’s questionable communication choices.) An unspoken theme is arguably being in possession of relatively little information (like, what’s going on with the person who is still waiting to find out if the vaccines are effective? And do people just not know that the vaccine reduces the downside of covid, even if it is still possible to get it? Or do all of these people know things I don’t?).
I wonder if much good could be done in this kind of situation with some kind of clearly independent and apolitical personal policy research institution, who prioritized being trustworthy and accurate. Like, I don’t trust the government or media especially either on this, but I and people I do trust have a decent amount of research capacity and familiarity with things like academic papers, so we arguably have an unusually good shot at figuring out the situation without having to make reference to the government or media much (assuming there aren’t more intense conspiracies afoot, in which case we will end up dead or tracking-deviced, I suppose). If I wasn’t in such a position, I feel like I’d pay a decent amount for someone to think about such things for me. I guess this is related to the service that doctors are meant to provide, though the thing I imagine would look very different to real doctors in practice.