The opening paragraph of the article:
"I'd like to begin by emphasizing that carbohydrate restriction has helped many people lose body fat and improve their metabolic health. Although it doesn't work for everyone, there is no doubt that carbohydrate restriction causes fat loss in many, perhaps even most obese people. For a subset of people, the results can be very impressive. I consider that to be a fact at this point, but that's not what I'll be discussing here."
And later on in the article:
"I think it's likely that refined carbohydrate and sugar can contribute to obesity, but by what mechanism? Insulin is not a compelling explanation."
I don't see a charlatan exposed here.
Guyenet's critique reminds me of a saying I heard a while back: Sure it works in practice, but does it work in theory?
This is pretty well known, and has a fairly simple mechanism. By imposing artificial restrictions on your diet (no carbs, no acidic foods, nothing brown to yellow in color), you reduce the amount of calories you can consume. I.e., where you previously saw "ooh, lemon cake, let me eat", you now say "no yellow food". Caloric consumption goes down, and so does bodyfat.
This is why basically all weirdo diets work in the short term.
The fact is that Taubes theories about insulin have been shown to be false. His theories that obese people retain more fat has also been shown to be false. His theories that obese people have a lower metabolic rate have also been shown to be false. He continues to push them in spite of this. That's the definition of charlatan.
Another experiment: go read this article of his. http://garytaubes.com/2010/12/inanity-of-overeating/
Then based on his presentation, state what you think his hypothetical fat person and thin person are eating. Most people come away with a completely wrong idea.
I agree that by itself, the one paper Taubes focuses on does not prove all that much. So what?
Taubes is using rhetorical tricks - in this case, throwing words at the reader, confusing the issue, and declaring victory, in an effort to prevent fanboys from catching onto him. It'll probably work, he'll probably make millions more selling books. Doesn't make him any less the charlatan.