I generally support vaccination and there is an argument that public health can sometimes trump individual rights or even health. That said, the example that has always bugged me though the default of giving babies Hepatitis B vaccine even if there is no possible vector for them to get the disease. The other example is chickenpox where we are trading off a potentially mild disease (everyone I know had it as a child) to the risk of getting it as an adult where it is more severe. These tradeoffs are not straightforward and the health authorities are also not transparent about how they weigh the risks.

I've also done something similar with my children. Make a determination for a specific vaccine and schedule. This is a combination of both weighing their health above public health and applying my particular circumstances (e.g. stay at home mom vs. daycare) to adjust the risks. They ended up getting most vaccines, just on a different schedule.