Your argument completely ignores the epidemiological evidence cited by Bennett, which tends to implicate Mycobacteria.
The article also clearly implicates factory farms as a cause for encourgaging spread of Mycobacterial infections in the cow population. In the old days, when people drank unpasteurized milk, it was more likely to come from the family cow or a small herd, with less chance of infection from other animals.
I completely agree that American medicine is often wedded to obsolete models of disease. Our extremely complex and normally brilliantly effective immune system does not foolishly turn on the body's own tissues for no reason. Many so-called autoimmune diseases may in fact be of infectious origin. There is also reason to suspect Mycobacteria as causes of arthritis and prostatitis.
MAP can hide from the body's immune system- within a part of the immune system (joggin my memory now)- also MAP does not have a regular cell wall like other bacteria (why called clear bacteria)