Mandatory Vaccinations

People with logical reason are easy to counter. People with religious/illogical reasons are impossible to counter and generally polemical.

In addition to this, religion is by itself a whole entity to be dealt with; logicality is not. You could be asking for A, another asking for B, things get messed up and the line has to be drawn. It currently is drawn, you're just not happy with it, and that doesn't mean it's wrong.
Vaccine serves to save human lives, whether you believe it or not, and we have all learned about the bloodshed when you pet religion the wrong way.
What's more, the vaccines proved to be effective enough with this exemption, so really, aside from certain people screaming for the same toy his brother got, it's not posing any real issues, which presumably are more important a factor.

As for the idea of equality itself, even if religious people were rightfully exempt from vaccines, it still does NOT equal giving the same right to the public mass. One kid exempt from vaccines could very well be the only one in his school, as opposed to what you're asking for: For each and every vaccinated person, there's one who would choose to opt out, which is quite more headaching if you ask me.

Disclaimer: I'm only bullsh'itting my personal thoughts, like them, dispute them, or leave them. This isn't the place to talk about religion.