In general, I'm in favor of vaccines. They are one of humankind's biggest health accomplishments of all time (along with soap, dixie cups/drinking fountains, toothbrushes, and antibiotics).
Every intervention, really every action we take, has consequences. If we breathe air, we generate by products (carbon dioxide, etc) that can catch up with us. If we pave roads, we reduce the capacity of our earth to purify water. On the whole vaccines have been hugely beneficial with very few adverse effects.
Since vaccines are a bit mysterious and somewhat invisible, it is easy to blame them for some mysterious maladies -- like autism. While it is possible, it is quite doubtful. Thankfully a recent book defends vaccines against this rampant urban legend. For more, please read http://www.nytimes.com/2009/01/13/health/13auti.html.