Modern medical Science has indeed come a long way, and most scientists will acknowledge that we have a long way to go. Unfortunately people always want certainty, when there is none. Its always a matter of weighing up the evidence, and making a choice based on the whether you believe the benefits outweigh the risks.
I think the benefits of vaccinations, for some diseases, absolutely outweigh the risks.
I make my decisions on individual vaccines, not vaccines as a whole, and the evidence for the efficacy of those particular vaccines, as well as evidence of risk. I then weigh this against the risks of contracting the disease the vaccine is for, I look at the likelihood of contracting the disease, and the likelihood of an adverse outcome from the disease.
I also find archeology fascinating, and think we can learn a great deal from ancient civilizations.