From the New York Times article:

On the one hand, we've been told with almost religious certainty by everyone from the surgeon general on down, and we have come to believe with almost religious certainty, that obesity is caused by the excessive consumption of fat, and that if we eat less fat we will lose weight and live longer.

Either Taubes is throwing out a straw man here, or his opponents are ridiculously simplistic. It's pretty well established that some fat can be good for you, and length of life is based on a whole ton of factors.

The problem with nutritional science is that you don't need any sort of expertise to get a platform, you just need strong opinions. See both Taubes and his opponents. Those kinds are always trying to scare you into buying their latest book by simplistically dividing food into "good" and "bad" types, and insisting you'll die if you keep eating the bad ones. Not to mention lose weight if you eat the good ones.

Weight management boils down to simple physics, namely the First Law of thermodynamics. If you consume less energy while spending more (via exercise mainly), you'll lose weight. One calorie is completely interchangeable with another calorie, it doesn't matter where it came from. (The exception being that it's easier to add muscle mass by eating proteins.)

The hard part about losing weight isn't knowing what to eat, it's having the willpower to eat less (or exercise more). Of course, you can't sell a book by telling everyone "we're fat because we have no willpower". "We're fat because we've been lied to", however, will sell.

(EDIT: I'm going to add some clarifications on my position here because the feedback shows that I've made my position seem more extreme than I intended.

First, I shouldn't have said it was simple, it's not.

If you eat just until you're full and you get moderate exercise but you're still overweight, you should talk to your doctor. You may still need to change your eating or exercising habits, but you should do research first, and not make any sweeping changes all at once. And you should never have to be constantly hungry, or end up having to eat almost nothing. Both outcomes are extremely unhealthy.

Changing your habits is always difficult, and that's where the willpower comes in. It should only be needed until you settle into your new habits, though.

I'm not trying to compare the metabolisms of separate people. Some people can eat a lot more than others and maintain a healthy weight.

I'm not trying to say you can cut food willy-nilly and still be healthy. I'm not trying to use energy balance as a curiosity stopper. I'm trying to use it to combat claims that you can eat as much "good" food as you want as long as you avoid "bad" food.)