It is rather hard to argue against the germ theory with regard to such diseases as AIDS, Pneumonia, STDs etc, esp with evidence of contagious human to human transmission, yet you just have to look at such entities as "post-lyme syndrome" to see where it can be arguable as to the nature of the disease.
For those that are unfamiliar, several large randomized studies have shown that further antibiotic therapy has been found to be no better than placebo in patients with a history of lyme disease and persistant symptoms. Yet some infectious disease specialist still prescribe long term antibiotics. Unfortunately, our ability to detect the spirochete is dependent on the detection of antibodies against it and not direct presence of the bacteria or its antigens.
Many diseases are not due to infectious agents such as bacteria, fungi, parasites, viruses or prions. Yet some may be initiated by exposure, and some where it is later found to have a connection, such as Helicobacter Pylori and peptic ulcer disease. There have been some diseases which links have been suggested but evidence has not been found, such as an infectious cause for coronary artery disease.
Ultimately, every theory is subject to debate and modification over time, luckily most changes become ever more minor with successive revisions.