The difference is, is that there is no evidence to support the theory that Autism is caused by vaccines, so it is not a credible comparison.
There is plenty of evidence that shows that vaccination does prevent illness, such as whooping cough. There is also a very high chance of adverse outcomes and death, from people contracting whooping cough. Particularly in very young babies.
We do not have natural immunity to any of the diseases that we have vaccinations for today. People just simply died, or suffered adverse effects, such as blindness, crippling, etc, in the past.
We don't live in a perfect world by any means, but I for one, do not want to go back to the days of preventable disease epidemics, that maimed and killed so many. The good old days before vaccination, were only good for those that were lucky enough not to contract any of the worst diseases.