Anyone have any thought as to how safe immunizations are these days? Feel strongly one way or the other?

My son will be five in June and ever since he was about oh-6 months old my husband and I decided to opt out of the immunizations. That was right about the time when the whole Thymerisol issue and Autism came about, so we just didn't feel comfortable enough doing it.
Now my son will start school in the fall and the principal told me that I just had to sign a waiver to get him started. (And the physical of course.) But she also said that if they had an outbreak of any kind he would be asked to stay home. I don't really have a problem with that.

Anyone gone through this already? Anything I should know before he starts school? Im just so worried about it all anyway, lol. He is my only child and my baby, so of course Im a wreck.