Andrew Wakefield (a gastroenterologist)...plus the 13 other researchers involved in the study were not even talking about the MMR vaccine.  It was a paper about the link between stomach problems and autism.  The reference to MMR and autism was only the experience of many of the families they spoke to about when the autism (and stomach problems) started.  They heard the same story over and over from families about how the autism symptoms started very shortly after the MMR vaccine was given.

In my mind Wakefield and company were vindicated when the CDC whistleblowers came out and said that the CDC falsified data in the study they published saying there was no link between MMR and autism.

The odds are stacked against anyone who questions vaccine safety...the drug companies have a lot of money and they throw it around liberally.  No one wants to kill the goose laying the golden eggs...