Parents are responsible for the health and wellbeing of their children as they are most likely their primary caretakers. As such, not vaccinating said child leaves them at risk for serious and preventable illnesses, which in some aspects can be seen a child abuse. Children who are not vaccinated need to be taken out of their dangerous environment and ensured that they're put into the right hands so that they can experience a healthy childhood and grow up to be normal and (ideally) productive adults to contribute to our future as a society.
Many of these Anti-Vaxxers are likely trying to do the very best for their children, albeit in a misguided way. Taking the children away would add more to an already burdened system potentially moving children from a caring home to those who might not care or be abusive.
The vaccinations can not be allowed to be skipped however and the parents must be overruled in this case. If vaccines were no longer mandatory then the majority of people would go for the easier and/or less expensive choice especially if they were deluded by the anti-vaxxer propaganda.
Large portions of the population going without vaccines is just asking for a massive epidemic to occur. The threat of such is to disastrous for society as a whole to be allowed.
It's true that some vaccinations children should get to help protect them, and it's also true that parents should do what they can to protect their children. However, taking away a parent's child just because they don't give them vaccinations is both a violation of ethics and freedom. If we go so far as to say that parents must conform to all of these governmental defined rules in order to keep their children, then we become a communistic society where, in essence, government raises kids in the way it thinks befitting. That is a dangerous world.
Children depend on their parents and their parents have a say in how they are treated. It's not abuse to not give them vaccines; 200 years ago such vaccines did not even exist, so while 200 years ago a parent could abuse their child in may ways, the best parent of all time couldn't vaccinate their child... It makes no sense to say that NOT using a technology that is beneficial to the child, is abusing it. What next, confiscating children whose parents don't get them the latest educational software on their iPad?
The most charitable thing I can say about parents who don't vaccinate, is they are naive and at least somewhat selfish. The best decision for the society should be, I think, eagerly vaccinating. I don't wish a plague on them, and certainly not on their innocent children, but I hope they will change their minds.
That said ... Don't take kids away for that. It's a parent trying to do what they believe is best for their kid. If necessary for the rest of society, you might exclude them from things like public schooling because of it, but even then only if necessary.
Parents have an impact on their kids. They impact their diet, their education, their values, ethics, morality, habits ... And health. To decide "for this specific case, we're going to override parents' wishes" is a genuinely slippery slope that will lead to additional encroachments on parental interaction with children, that is a significant part of what being a free person is supposed to entail.
They should only be taken away on the temporary occasions required to administer the vaccines, then promptly returned to the parents. Only take them away permanently if the parents then try to hide their residency in an attempt to prevent vaccination.
Government should only use a minimum of the force required. It is not necessary to take the kids away permanently, only temporarily whenever they need a vaccination. In fact we don't even really need to take them away if the doctors are willing to go with social services to the home and administer the vaccination right there and then leave.