When I was going to school from K-12, I had faith in science. Yes, I know, the fundies are going to have my head for that line, but bear with me.
I sincerely believed that scientists were altruistic researchers who wanted to add to the body of knowledge in the world, and maybe get a little scientific glory for themselves. Once in college, I learned that I was very wrong. While there are some of those starry-eyed researchers out there who want to find real truth, many of them are primarily seeking a particular outcome, no matter what the facts say.
Data is massaged and manipulated. Studies are well-crafted to ensure a particular outcome. Experimental results that do not benefit the desired outcome are often tossed out completely. Basically, most of these guys want to be able to prove their point at all costs, often because the money's flowing from someone who says, "Give us THESE results."
There are no video cameras in the lab to ensure that the correct numbers are written down. There is no way to check and see if mice with undesirable results were quietly discarded. If I'm in a laboratory, and I count X number of bad results, I can write down Y results instead. In my last job, I was actually encouraged to alter data so as to avoid having to do something about products that were out of spec.
When you're selling an idea, the real motives are often hidden. For example, U.S. citizens were informed that Iraq was harboring weapons of mass destruction, and that Iraq was directly tied to the events of September 11, 2001. We now know that this was not the case, and the true motives behind selling the idea of invading Iraq were probably something quite different from protecting U.S. citizens from terrorism.
Those selling the idea that fat is bad and unhealthy are not motivated by an altruistic concern for people's health. If you find that a study is funded by the diet industry, you will probably find that its results are quite beneficial to the industry. This allows the industry to continue selling products and services that do not work, especially ones that work in the short term, but eventually fail. Built-in repeat customers are quite profitable, after all.
This makes me wonder how many other ways we are kept "sick" by the pharmaceutical and other industries that fund medical research. I remember when they changed a number, and suddenly a lot more people had high blood pressure. I had just gone to my (former) doctor in an extreme amount of pain from an infection, and my blood pressure of 140/90--higher than I'd ever had it since one awful night of agony in the ER*. My history of low-side-of-average readings and current stressful state didn't matter to him; he saw an opportunity to prescribe, thanks to the drug reps that pepper every available surface of doctors' offices with free gifts. I dug in my heels and refused to be put on blood pressure medication at the age of 28. Amazingly, I was fine at my next visit, since my pain was relieved, and I've been fine since. Had I been put on the medication, I would have suffered all kinds of side effects, and would have derived no benefit.
I think what aggravated me the most about it was that, instead of treating the cause, which was my pain and infection, he wanted to treat only the symptom. Artificially lowering high blood pressure is not necessarily a useful thing to do, and if a cause can be identified, it makes far more sense to fix THAT problem instead. Remember the old joke, "Doctor, it hurts when I do this"? Doctors today say, "Oh, here's some pain medication," when they should be saying, "Stop doing that!"
Of course, scientists have been getting it wrong all on their own for hundreds of years without the help of pharmaceutical grants. Every time I read about the medicine practiced even a hundred years ago, I get the feeling that they just made stuff up and declared it to be true. "Vapors", "humors", and "hysteria" are just a few of the ridiculous ideas that took way too long to overcome, and at the cost of many people's health, freedom, and lives.
People have been resisting change in scientific thinking for as long as science has existed, too. If you grew up thinking that a bat was a bird, you're going to fight pretty hard against someone who says it's actually a mammal. Add to that someone's financial stake in keeping the status quo, and you have our current situation of making sure that fat continues to be thought of as an illness. Ill people need medicine, surgery, treatment. If they realize that they can forgo these things, a lot of interested parties are going to lose a lot of revenue.
Follow the money, and remember that science is ALWAYS to be questioned. Learn to critically examine new studies--not just their abstracts, but their methods and data as well. If you're not comfortable doing these things, then at least have a look at others' interpretations of them; try to find the other side of the story. Sandy of Junkfood Science does a good job of doing this for us, and there are plenty of other authors out there doing it too.
*It turned out that my gallbladder was acute. I'd never even had an attack, so this was quite the surprise. They scheduled surgery asap, then rescheduled it even sooner after the bloodwork came back. Yikes. That was the worst physical pain of my life.