A nontrivial amount of opposition to vaccines comes from communities, both online and in person, that circulate accounts of atrocities committed by authorities. Naturally, accounts of mistreatment, whether or not its systemic nature is seeming or proven, will weaken trust in institutions. Good actors are always having to compensate for the activities of bad actors, even if those bad actors were in the distant past.
But it says a lot about our society and the quality of our institutions that the lack of trust isn't just among groups that have themselves been mistreated, but is also found in others who observe these issues of social justice from a position of relative privilege. Based on their observations, some of them have concluded that it's far from certain that malice, corruption, or lack of transparency don't factor into the mainstream stance on this issue today, likely because there is evidence that similar factors were at play in similar issues in the past, and the incentive structure of actors and organizations need not have meaningfully changed.