A "mandatory" flu shot every year angers me, especially when the flu strain easily changes and the manufacturers are basically guessing every year what to formulate.
Even very pro-vaccine people and doctors question this type of "mandate." It was only a few years ago that my internal medicine doctor, as well as my pediatrician, told me that only "high risk" people should receive flu vaccines (though you could do it if you wanted to). Am I now supposed to have amnesia or believe that the science has drastically changed that quickly? C'mon!
I would explore the exemption info a couple of the other moms mentioned. And no, just because you use a religious exemption does not necessarily mean that future vaccines void it (that's an urban myth). It really comes down to very specific state laws, that vary state-by-state. I have read that New York is one of the strictest states on religious exemptions, but I don't know about CT.
I'm not anti-vaccine but I also believe that our children are not pin-cushions subject to every profitable idea that pharma can dream up. And yes, vaccines are profitable, contrary to another urban myth that they are not. They are one of the few growth sectors of the industry. And most ped vaccines are not subject to the same product liability laws that every other product in this country is (see the recent USSC case known as "Bruesewitz": http://www.supremecourt.gov/opinions/10pdf/09-152.pdf) . Instead you're stuck going to a "vaccine court" - which is not a traditional court of law at all - no jury, different rules, etc. Awards are paid out of a fund created by a tax on every vaccine administered (not paid by the pharma co that made the product). Therefore, where is the incentive to create the safest product possible? (see Justice Sotomayor's dissent).
Again, I'm not anti-vaccine, and we homeschool. But it is still my belief that we have to resist some of these more blatant affronts to parental rights to direct the health care of our children (via excessive regulation and fear tactics), before we lose them all.