Why do you say that? It has been reported as extremely successful for treating some conditions -- c. difficile, or something like that, if I remember correctly. Like, one treatment and the problem is permanently cured for the vast majority of patients.
I understand your hesitancy to believe everything that comes from the medical establishment. But feces are not a product sold by drug companies; they're Mother Nature's specialty! All natural, and of profit to no one.
Anyway, I think I read somewhere that Fecal Transplantation isn't likely to be effective against candidiasis, although I'm not sure that that's much of a certainty. It might be worth some medical research; I dunno.