Because that’s what naturopathic medicine preaches. What you are talking about is not “naturopathy.” By definition naturopaths don’t believe in evidence based medicine. What you are describing/looking for is part of standard medical practice. Look up FODMAP diet for IBS as an example. Microbiome research is also opening up whole new theories on the role of diet and medicine.
Herbal medicine vs. prescription drugs is pure chemophobia btw. Many prescription drugs are derived from plants and fungi (eg many antibiotics, anti-arrhythmics, anti-cancer drugs). I recommend this article for some perspective http://www.slate.com/articles/health_and_science/medical_examiner/2013/02/curing_chemophobia_don_t_buy_the_alternative_medicine_in_the_boy_with_a.html