Treat the cause, not the symptom
Treat the cause, not the symptom is a phrase often used by alternative medicine practitioners. They use it to mean that while evidence-based medicine only treats "symptoms" like pain, alternative medicine treats the underlying cause of the symptoms.
 A decent thought
Treating the cause is what every medical practitioner should aspire to do. For example, if someone has a disease caused by poor nutrition and lack of exercise, it makes sense to fix their lifestyle rather than taking some pills to make their symptoms go away.
 Causing far more problems than it solves
However, the problem is that very often the "causes" described by alternative medicine practitioners are old wives' tales with no basis in reality – such as "energy" imbalance, toxin overload, miasmas, and many others – and are often ascertained by means of bogus diagnostic techniques.
For instance, some claim that germs are only symptoms of infectious diseases, not the cause. And what is the cause, if not germs? Well, the real "cause of all disease" will vary wildly depending on which practitioner you ask. Some may claim that it is miasmas, while others will state that it is humoral imbalance, the result of dehydration, pH imbalance, toxins, candida, or any of many other contradictory "causes". In other words, generally those who claim to "treat the cause" will employ useless diagnostic tools designed to sell you "cures" that don’t work for problems you haven’t got.
Though this phrase is frequently used in a legitimate way, it is, because of its constant use by promoters of unproven upto now and often proven-wrong treatments, often a red flag of quackery (as has happened to the word "holistic"), given that the said "causes" so often are pseudoscientific or supernatural in nature.
Another problem with this concept is that despite the best efforts of medical science, the causes of many diseases are still not known. In this case, treating the symptoms is the best possible course of action until the day the etiology of the disease is discovered. One useful analogy here is to imagine primitive humans using water to put out fires before understanding why this worked. Likewise, the mechanism of action behind many drugs is not fully understood, but they have been tested in clinical trials and nevertheless we know that they work even if we don't know how exactly. Obviously it's better to know the particulars, but sometimes there isn't anything else to go on. For example, many psychiatric drugs work this way, because of the difficulty of cracking someone's head open to
feast on the goo inside see how exactly they bind to receptors on neurons. We believe, for example, that antipsychotics work by reducing levels of dopamine. We don't have hard evidence that this is indeed their mechanism of action, but it's plausible given their design and what we know about neurochemistry, and we know they work fairly well. To a person suffering from schizophrenia, the mechanism of action is immaterial as long as they reduce their symptoms and have tolerable side effects.
One more major problem is that many diseases do not in fact have one cause but are multifactorial. Heart disease, diabetes, alcoholism and many other diseases result from a combination of several factors that may not all be present in a given individual, including genetics, lifestyle, diet, socioeconomic class and so on. This does not jibe well with the many alternative modalities which promote the idea that all disease stems from a single cause (e.g. a vertebral subluxation or a focal infection in the mouth). How these practitioners would attempt to treat a disease with many causes when their belief system insists there can only be one single cause of disease is a logic bomb of the calibre that makes robots' heads explode on Star Trek.