I saw that Common Dreams article and thought it was interesting. But it has to be noted that the parts of the same area were in some ways more polluted and toxic than what we see now. Difference being that up until the 1950s no one was studying the health effects. Coal tars, benzine, phenols and early disposal of toxic wastes and all sorts of other general offal and crud were freely dumped on the land and in the rivers. The same land the poor and the workers in the factories and processing plants lived and often the same water they drank.
Word was you could tell what each plant was doing by the color of the river beside it and workers were identified by their type of 'industrial cough'.
The difference is that nobody was studying the health effects and they didn't have Super-fund sites or hazardous waste dumps. They had the surrounding land and the river. Nobody considered doing it any other way. If your kid was retarded or got sick and died it was just part of living in an industrialized age. 'Hire people with hooks' and 'company stores with company credit' were standing jokes.
We are more aware of the damage and potential for biological damage because we have the tools and have taken the time.
As for the Amish.
"Could it have anything to do with the fact that the Amish haven't (historically) gotten vaccinations? Or that they don't farm with chemical fertilizers, herbicides and pesticides?"
Nobody knows for sure. The studies are incomplete. I think several recent studies have pretty much delinked autism from vaccines and mercury within vaccines. Generally not being vaccinated or vaccinated with a vaccine that doesn't contain mercury doesn't seem to change the prevalence.
Also the rates of autism don't seem to be in any obvious way linked to pesticide or herbicide exposure. But, as far as I know, there haven't been any large studies designed to show any connection or non-connection. The anecdotal evidence doesn't show high rates of autism in people with these chemicals in their bodies. There are a whole lot of other really bad effects, including liver damage and birth defects, but autism isn't near the top of any list I remember.
IMO the best bet is that the Amish may have a genetic factor that protects them. This makes some sense because the Amish are fairly tightly intermarried. With a limited number of families and the vast majority of children being a product by crosses within this narrow community. This near inbreeding would be constantly making genotypical, hidden potential genetic tendencies, into phenotypical, clearly physically apparent, manifestations.
It also makes sense that autistic children would be kept by the tight sexual mores from reproducing. Their genetic line, and its tendency to be susceptible to autism, would die out as they naturally age and in time the population would become entirely free of the genetic tendency to succumb to autism.
This is the classic methods farmers have used to clear the susceptibility to any disease from a flock. Recessive genes lurk within the genetic code. Cross breeding to closely related animals allows the recessive genes to manifest themselves and become clearly visible. This allows the farmer to keep the lines prone to the disease from reproducing and to select the less disease prone stock and breed them instead.
The Amish are farmers and well aware of how to breed healthy stock. I wouldn't go so far as to call it a selective breeding program, and it doesn't even resemble eugenics, but it makes sense that the surrounding Amish society to want the good-looking healthy guy to get together with the good looking healthy girl. And to encourage them to have a large flock of children.
Any children with autism that might show up would be loved and cared for but they would also be encouraged to stay celibate and to avoid having children. Using this alone it wouldn't take many generations of these social pressures to eliminate the tendency to develop autism.
If true, and just because it makes some sense to me doesn't make it true, the Amish having few autistic children could be a result and benefit of having a closed and relatively inbred society. I suspect that soon enough, in a few years, some scientist will present the world with a study supporting this argument, or not.