Time Magazine’s cover story this week is titled “Why Exercise Won’t Make You Thin.”
I think Gary Taubes first wrote about this in a book I read called Good Calories, Bad Calories 
Here’s an excerpt on this topic from an article Taubes wrote in New York Magazine:
The one thing that might be said about exercise with certainty is that it tends to makes us hungry. Maybe not immediately, but eventually. Burn more calories and the odds are very good that we’ll consume more as well.
John Cloud, author of the article in Time Magazine, is saying the same thing:
The basic problem is that while it’s true that exercise burns calories and that you must burn calories to lose weight, exercise has another effect: it can stimulate hunger. That causes us to eat more, which in turn can negate the weight-loss benefits we just accrued.
Cloud cites a study from the peer-reviewed journal PLoS ONE (PLoS is the nonprofit Public Library of Science). In the study, 464 overweight women who didn’t regularly exercise were randomly assigned to four groups. Women in three of the groups were asked to work out with a personal trainer for 72 minutes, 136 minutes, and 194 minutes, per week for six months; women in the fourth group were the control and were told to maintain their usual routines.
What did they find?
On average, the women in all the groups, even the control group, lost weight, but the women who exercised –sweating it out with a trainer several days a week for six months — did not lose significantly more weight than the control subjects did.
Church explains this in terms of compensation:
Whether because exercise made them hungry or because they wanted to reward themselves, (or both), most of the women who exercised ate more than they did before they started the experiment. Or they compensated in another way, by moving around a lot less than usual after they got home.
Another study by Dr Neil King, from QUT’s Institute of Health and Biomedical Innovation, conducted in collaboration with the University of Leeds in the UK, and published in the latest edition of the International Journal of Obesity, supports Taubes’ argument.
In this study, 35 overweight and obese people from the UK, went on a 12-week supervised exercise program that was individually tailored to expend 500 calories per session. During this time their weight loss and behavioral outcomes were monitored.
Dr King found that the role of exercise as an effective weight management method could be undermined by ‘compensatory responses’ such as a person’s increased hunger and food intake as a result of their increased energy expenditure.
King says:
People, who we refer to as compensators, are those who compensate for the increase in exercise-induced energy expenditure, by adjusting their food intake. For some people this might be in responses to an automatic biological drive, whereas for others it might be a deliberate reward-based increase.
Dr King said what this study showed was that some individuals were predisposed to compensatory responses, rendering them resistant to the theoretical weight loss benefits of exercise.
Taubes explains this in Good Calories, Bad Calories:
What may be the single most incomprehensible aspect of the last half-century of obesity research is the failure of those involved to grasp the fact that both hunger and sedentary behavior can be driven by a metabolic-hormonal disposition to grow fat, just as a lack of hunger and the impulse to engage in physical activity can be driven by a metabolic-hormonal disposition to burn calories rather than store them.
He continues:
By this logic, those who become obese have a constitutional tendency to fatten, whereas those who remain lean have a constitutional tendency to resist the accumulation of fat.
I think that Taubes’ argument is valid. I can see it with my clients. Some people have a metabolic-hormonal disposition to accumulate fat while others are more inclined to burn fat and build muscle. So I think the information is useful to help people understand underlying factors that may have caused them to gain weight and get out of shape.
But while some people may have been more inclined to accumulate fat before we started working together, more often than not, they are successful at losing fat and building muscle through diet and exercise once we begin training… especially when the diet is low-carb and the exercise is resistance training combined with high-intensity intervals.
Techniques like using a food-diary to become conscious of food choices, increasing fat-burning muscle with resistance training and performing high-intensity intervals are all very effective for fat loss.