I think it's usually more of a case that the docs were not taught any of these things in medical school, so they just don't know. Most doctors are pretty ethical people, I think, and wouldn't withhold a beneficial treatment just because they don't make money off of it. Nowadays, student doctors are being taught more about the alternative/complementary therapies out there, but we're still a few years from the point where these treatments will be instated on a more regular basis. That's why patients have to do their research and bring back what they learned to their doctor. But it's VERY important to tell your doctor what supplements you are on! You don't want to be taking such high dosages of calcium, for instance, that you're going to develop hypercalcemia.
Point being: do your research, be pro-active, but keep your doctor involved! Docs don't know everything, but they have at least 12 years of post-high school education under their belts. They've memorized thousands of drugs, drug side effects, drug interactions, etc.; if they are unfamiliar with something you are taking, take the opportunity to tell them what you've learned about it!