Toleration of those who don’t conform is simple. Just as someone cannot force another into joining a religion they do not practice, someone can also not be forced into something that would only affect that individual privately. Vaccinations are proven to be a beneficial ward of potentially deadly diseases, but it’s not something that can be forced onto someone.
The Commonwealth is a structure built so that individuals may focus on preserving and advancing their own Civil Interests, such as life, liberty, health, and property. Becoming vaccinated surely helps preserve the civil interest of health for an individual, but it is still up to that individual to choose whether or not they want to preserve that civil interest in that way. The Commonwealth is structured for providing an environment where people can have access to ways of advancing their own health. However, just because that easier access is provided doesn’t mean that it has to be accepted. An individual is allowed to refuse something, even though it might benefit them, based on that individual’s own beliefs. This refusal should be tolerated to the extent in which the consequences of that action only affect that individual, as the refusal at that point won’t be affecting the civil interests or rights of anyone else.
Vaccinations, however, don’t just benefit the individual, but prevent diseases from being spread that could possibly affect the liberties of others. A disease that someone carries because they are unvaccinated can place others in harm’s way, even take away their lives. Because of this, a private matter such as choosing not to be vaccinated can start to have some consequences in the public sphere. I pose it is up to the structure of the Commonwealth to create a way to tolerate such individuals, or rather, prevent their private matters from becoming public issues, for both the sakes of those who choose to remain unvaccinated as well as those who might be affected by them. The easiest way to do this is to have being vaccinated as a requirement for participation in and access to the services of the Commonwealth, such as schools, workplaces, and recreational facilities, since something as simple as exposure to an unvaccinated person can create a public issue. Complications also arise when trying to restrict access to certain places that cannot easily be restricted, such as a public park. At that point, the Commonwealth could restructure to protect those who choose to go unvaccinated, but there is still responsibility that lies with that individual too. Say that individual chooses to ignore these restrictions placed by the Commonwealth and creates a public issue that affects the rights of someone else. Then that individual is liable to face the consequences for affecting those rights, whether they be from that others or from society itself. Really, this is a dangerous and cautious life to lead, but it is still their prerogative to do so.