I think that we'll eventually learn that autism has multifactorial causes, and that not all autism is alike.  Just as many young children regress into autism, I have seen some who present as autistic and seem to mature out of it.  It's like they come into their own.

Some have hypothesized that autism is an extreme form of the male brain.  I notice that many (most?) men don't make sustained eye contact when listening to others.  It's not out of the ordinary for men, but if women made as little eye contact and displayed as little affect as many men, they would be considered socially impaired.  There's a lot more to autism than eye contact, obviously, but there are some normal male relating patterns that do seem exaggerated in autistics.

In addition to the genetic component, including the father's age, and some immune responses in pregnant women, I think eventually we'll find some connection to environmental neurotoxins.  There is so much crap in our textiles, furniture, etc., and some of them have been introduced recently enough that they may account for some of the increased incidence of autism.