Circumcision is a medical procedure for which there are costs, benefits, and risks.
It is a medical procedure but rarely a medically-motivated procedure. Costs, benefits, and risks are not weighed. Tradition is the deciding factor.
In contrast, vaccinations have a well established medical purpose. Vaccinating your kids not only reduce their risk of disease, but also helps teachers and other kids your kids are near all day in school, and those kids' and teachers' vaccinations reduce the risk for your kids. Children are routinely in closer proximity, and are generally less hygienic, than adults. There is no alternative to mandatory vaccination to take advantage of
herd immunity. Smallpox was eradicated not with microscopic bombs, but rather through intense vaccination efforts. What happens when people decide based on ignorance that immunizations are unnecessary? One infected person (or animal carrier) introduced into a population with insufficient immunization can cause unnecessarily large outbreaks, and are more difficult for public health agencies to contain once they get started: http://en.wikipedia.org/wiki/Measles#The_Americas
Legitimate medical reasons for circumcision should be handled on an as-needed basis. It isn't very difficult to distinguish rare instances of medically-recommended circumcision from routine circumcision: "Oh look, it's a boy... get the knife!" The issues of penile cancer and easier HIV transmission need not be addressed at birth; they can both wait until adolescence. You won't get prostate cancer if you have that removed, so perhaps we should do that at birth, too? Baloney.
Parents make religious and ideological decisions for their children? Some parents turn their children into little robots, and more try, and that's unfortunate, and not easily dealt with because of the difficulty of determining what decisions are necessary for the welfare of children and which decisions are excessively restrictive or attempts to instill propaganda. However, the issue of physical mutilation is quite clear, and in that realm it is easy to distinguish what's (medically) necessary from what amounts to culturally-motivated branding of infants who can't possibly understand the culture which seeks to brand them.
Is there serious physical harm? Not in most cases. Neither would there be serious harm by tattooing infants, giving them 12 ear piercings and a grommet in each ear. I doubt most people would appreciate being stuck with ears topologically indistinguishable from doughnuts just because their parents thought it looked cute, or because their parents thought it was necessary for metaphysical reasons.
We cannot know what traditions a child will believe in when he or she reaches adulthood. Routine circumcision, tattoos, piercing, and surgical implants for children are not acceptable if our goal is to raise children who think for themselves, who may, and should, choose freely what to believe in and what cultures to identify with when they're adults. Sadly, too many parents agree that children should be financially and socially independent from their parents, yet become distraught if children exhibit spiritual or even philosophical independence.
