Folks living on farms or in the forest generally don’t have autoimmune problems because they have constant exposure to animals, a wide variety of plants, etc. On average (especially the peasants) they have poorer health than folks living in cities, but the distribution of health problems is fairly different between the three groups.
Deadly plagues (viral and bacterial) have ripped through through and decimated agricultural societies relatively often, at least in the past couple millennia. Many crippling diseases have also been endemic in many places (especially tropical regions) as far back as we have records. Modern medicine and lifestyle (indoor plumbing, vaccines, antibiotics, refrigeration, mosquito control, medicines for killing parasites, ...) have done an amazing job preventing those in wealthy countries.
Does anyone wonder why we have antibiotic resistant bacteria? I thought that was pretty widely understood (at least by those who accept the science of evolution)...