I don't think it's half as bad as you seem to think. My wife's an NP, so I have an inside view of Syracuse, NY's medical situation. There's two issues at hand:
1. The quality of evidence for most supplements ranges somewhere between Bigfoot and Flat-Earth society. That's not to say it's all bad, but it's generally unstudied and unproven.
That being said: it's standard practice to strongly recommend vitamin D supplements for us northerners. That's reasonably new, high quality supplement data and it's not ignored. There's no bias for these types of medical practitioners, the data's just not there.
2. A lot of older docs are untrained when it comes to new studies about various things: pain meds (don't use them), alternative pain management (can be useful), H. Pylori (a proven explanation for stomach ulcers). These docs don't keep up to date. They're otherwise excellent doctors. Most of them care deeply about their patients and are fiercely defensive of them and their care (exceptions abound, but giving people the benefit of the doubt is a good way to live life a lot happier).
There's tons that's wrong with our medical system, try not to generalize it too far.
Also tell your doctor about ALL supplements you take. Some can react terribly with other medications and supplements.