There's a website called NutritionFacts.org that is not funded by the big Pharma companies or by big medicine; instead it is funded through donations. Check it out! And lest you think the media intentionally mislead you (as some high-raking political figures would have you think), read this post from today. Seems the problem begins a lot closer to the source—the researchers themselves and the sources of their funding. But ultimately, it's also what gets published. This final paragraph of the cited article sums it up:
I think the biggest problem with the way the media reports on medicine, though, is the choice of which stories are covered. In 2003, for instance, SARS and bioterrorism killed less than a dozen people, yet generated over a hundred thousand media reports, which is far more than those covering the actual greatest threats to our lives and health. In fact, ironically, “the more commonplace the cause of death, the less likely it is to be covered by the mass media.” Our leading killer is heart disease, yet it can be prevented, treated, and even reversed with diet and lifestyle changes—now that’s what should be front page news.