Actually, you don't ever find proof of anything in science. Hypotheses can only be disproved. The Wired article mentioned this as one reason that parents are suspicious of scientists when they talk about this--they use language like "no connection has been found," and people think that means they're beating around the bush when in fact it just means that a reasonable person can never be 100% positive about anything.

(By the way, I think it's very likely that the vaccines=autism idea was kick-started by the fact that people noticed autistic symptoms in their kids shortly after vaccination. That's another correlation/causation issue; signs of autism tend to show up when the kid is about three, which is around when a particular batch of vaccines is recommended.)