Respecting human rights and self-autonomy is not the same thing as removing rights from people to benefit the companies/government and I wish people would stop arguing in bad faith that they're remotely similar.
It is a problem when someone wants 'autonomy' in order to enforce reduced 'right's on others, or another way, my 'autonomy' is greater than your 'autonomy'.
So, lets say I'm commanded by my god to enforce that you must have kids. And I get enough people together to secede, in order to enforce these beliefs onto others. Then the people caught in this situation do have rights taken away.
Or, other people cross dressing offends me, thus I should have the right to pass laws to prevent them doing that, my 'autonomy' outweighs theirs.
It does get confusing, when some groups say they want 'autonomy' over their body when it comes to vaccines, but when it comes to 'autonomy' over having kids, suddenly it is a metaphysical law from god that can't be compromised.
Both are cases of bodily 'autonomy', and one group believes since it is a law from god, that it should be enforced onto others by government laws, which is really taking rights away.
When the group that thinks your 'autonomy' is an affront to their god, and you become the problem to be 'removed', and they are now running the government, now the government is taking away rights and infringing on the individual's 'autonomy'.