Before I say anything, I think most FA groups are run by extremists. They're no better than any extremist from any walk of life, whether we're talking about environmentalists or the KKK. Extremism is never good and often results in idiocy (or does idiocy lead to extremism?)
That said, it's a fact that some diseases cause obesity (and no, I'm not counting overeating as one of those diseases). Also, some people are just genetically predisposed to being fat. Why shouldn't we accept these groups? Even if the entire nation had a mandatory exercise program and rationed food supplies, some people would remain fat (but obesity rates would plummet, they just could never be 0%)
Why shouldn't people be accepting of fat people? What good does bigotry do?
I think diet and exercise are great things, but with every rational call for acceptance you'll always have stupid extremists. These fat acceptance groups aren't really looking for fair treatment.
Overall, claiming that moderation and exercise are bad ultimately doesn't do any good. Calling for people to be more accepting of fat people is great. I think they're doing more good than bad, because people think of fat people kind of how they think of smokers (that they did this to themselves, but that's sometimes not the case, unlike smokers)