When people don't vaccinate themselves they become a walking vector that affects society as a whole. Yes, personally, they might be healthy. But there's people out there who can't take the vaccines and should they get sick of COVID they could die. There's people out there who, even after being vaccinated, are still at higher risk should they get the disease (the vaccine doesn't prevent you getting sick, rather it makes it more difficult for the virus to transmit and lowes it's effectiveness and how dangerous it is for you). So people not vaccinating puts the whole of society at risk.
On the other hand, abortion is very much a familial issue. It affects the woman that is pregnant the most. The rest of the people around her are affected only tangentially, yes, the parents might want to become grandparents or the person that got her pregnant might also want to have a child. And those are inputs that are necessary when coming to the decision of performing an abortion or not.
Now, where does "your body, my choice" come into play? Do abortions cause the societal harm that vaccines cause? I don't think there's any evidence to this, it's all moral standings. But we legislate for everyone, we don't legislate for a group of people that happen to have a particular religious view of the world. Now, these people have a lot of power and influence and that's why their view is imposed on most of society.
Ultimately though, these issues are different and shouldn't be treated as mirrors of each others. I think that's a mistake.