The atkins diet seems like a good idea when you consider that fat is absorbed by your body in the last third or so of your intestinal tract. In the middle, complex carbs are absorbed. And towards the beginning is sugar. Sugar actually starts being absorbed while it's still in your mouth!
The idea is that the longer something takes to be absorbed by your system, the more calories you will burn to process the food. Therefore burning more calories. It's actually difficult for the body to turn animal fat and protein into usable fuel and human fat.
It's much easier for the body to turn complex carbs into energy, and thus easier for it to turn UNUSED complex carbs into fat. And of course, even moreso for sugar.
So the thinking is that you just avoid most carbs most of the time. Concentrating greatly on protein. And since protein is very rich and "satisfying" and stays with you for a long time, they tell you that you can "eat all you want". Because they assume no one can eat enough of "just protein" to actually gain weight, or even maintain it. You'd get very nauseous.
The problem is that that body cannot properly absorb and use protein without complex carbohydrates. Fiber, complex carbs, and the vitamins you get from them, are very important to the body.
Therefore something like The Zone diet or The South Beach diet seem a lot more reasonable to me. They take balance into consideration.