One of the problems with taking the "in your head" route though is that it discourages research into causes. And it doesn't explain why so many people have similar cases while coming from wildly-varying lives.
Sure. In-your-head diseases exist, and they're very real. Placebo effects, for instance, have been very conclusively shown to be extremely powerful - there's no question about the reality (though some still do...). But the odd recurrence of Epstein-Barr is very odd if it's all in your head.
Agreed - "in your head" doesn't mean what most people think it means, and is somewhat of a pejorative term. Such a disease is not really addressed by the psychiatric community at all, which disavows that the mind can have such a powerful effect on the body as to cause gross organic conditions like chronic pain (e.g. fibromyalgia), CFS, etc. However, there is nowhere else for the author of this article to point for ongoing research, most of which was abandoned in the 1960s. Such an ailment is not supposed to originate from the conscious mind at all, but from the unconscious, so:
1. The effects of the disease aren't in your head at all, they are very real, and
2. The cause happens to be in the brain rather than some other organ of the body, but it is not available to the conscious, thinking mind.
That doesn't mean that we should stop researching non-psychogenic causes for common ailments, as has been mentioned, ulcers and even some forms of CFS have been shown to have a clear cause and treatment. However, it seems a shame that this entire line of research has pretty much been abandoned...what happened, after all, to the hysterical diseases that Freud was successfully addressing in the early part of the last century? I doubt very much that they just stopped occurring.
(I have no idea if CFS is "in your head" or not. But even if it is, it can still be totally real.)