He is considering a wide range of chronic illnesses, some of which, like obesity, are not normally considered diseases at all. He's finding evidence, with detailed molecular genomic models, that many chronic illnesses are due to a breakdown in the body's conversion of Vitamin D. Cell Wall Deficient (CWD - missing cell wall) bacteria seem able to turn our immune system on its head, using it to attack our own tissues and protect themselves, The mechanisms used by the CWD bacteria including producing the bioactive 1,25 form of Vitamin D at excessively high rates.
See further for example Recovering from Chronic Disease - Sarcoidosis, Autoimmunity, AIDS and Cancers", Transcript of 18 June 2006 presentation by Dr. Joyce Waterhouse.
Diseases which this mechanism might explain, as mentioned on the above presentation, include inflammatory bowel disease (IBS), Chrohn's Disease, Ulcerative colitis, Arthritis, Lupus, Fibromyalgia, Chonic Fatigue Syndrom, Lyme Disease and Multiple Sclerosis.
Or, if you prefer video, see the YouTube video of a talk by Marshall, at Prof Trevor Marshall's AAEM 2006 Presentation.
He's not claiming that Vitamin D should not be supplemented by most people. He is claiming it should not be supplemented by those with such chronic diseases, because for them, Vitamin D (and Folic Acid and sunlight) make the problem worse rather than better.
And since he's further lobbying the FDA to not expand Vitamin D supplementation, because of the considerable risks it poses to those with such chronic diseases. Due to the current difficulties in diagnosing such diseases, the portion of the population afflicted with them, or at borderline risk for them, is no doubt wider than we know.
Yes, he did. and yet the epidemics of chronic disease, such as heart disease and obesity, are just getting worse.
His own words.
You may worship at his altar. I prefer to engage in critical thought.