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I agree with not letting these children go back to school. Putting these children's healths at risk is a serious case of bad parenting and I'm glad the courts have stepped in to look after these children where the parents won't
Surely what's the point of vaccination if it doesn't protect the children?
Herd immunity[1]. There is a threshold however, and if the vaccination rates get too low then herd immunity is less effective as the free-riders become a risk vector. In other words herd immunity works when the great majority is immunized and can sustain some free-riders but it can't sustain many free-riders.

[1]https://en.wikipedia.org/wiki/Herd_immunity

Vaccination isnt 100% effective. When people talk about herd immunity, the "free riders" it tolerates should be are those that were vaccinated yet it didn't take. If one of them gets sick, the disease wont be able to transmit to the others because of those that are immune. Adding other non-vaccinated people to the mix increases the odds that these vaccinated-but-vulnerable people will be at risk as the disease is able to find enough transmission to stay viable.
This was simply the normal for any child where I live when I was younger (we had a big Tuberculosis epidemic in mid XX century and some good practices from the time remained up to the present).
It is so sad that these kids need to be punished for the actions of their parents. They are now missing an important part of their education due to a backwards belief held by their parents. I seriously doubt any of these parents will take the time to home-school these kids in the correct fashion or at all. I am just in disbelief it needs to come to this.
Or even worse, they might use the time off to teach them about their beliefs about vaccines
There's a point where if something becomes a public health risk, it must be legally regulated. Those people are getting there.