actually you could turn your thought on its head and ask, why do things like microplasma affect some, but not others? is it genes as some would say? well maybe that's part of it in my opinion, but I believe it all comes down to the terrain... a weak and toxic body invites infection or multiple infections... the welcome mat is out for them. cleanse and strenthen the body and the "infections" will go away.
have you ever heard of a protit? some believe the seeds of "infection" are present in all of us in the form of the protit, just waiting to take hold when the body weakens... with our modern diets, drugs and lifestyle we certainly weaken ourselves and invite the infections in. so i have no doubt that in chronically sick people you will find micoplasma, lyme, bacteria and countless other "infections agents" buts its a bit misleading to say these agents are the cause of disease.
of course this is just my opinion (and I certainly didn't think it up myself), but, its something to think about.