It is certainly true that strong homeostatic mechanisms regulate weight gain in humans. Perhaps strengthening this homeostasis through exercise provides much of its protection against weight gain. However, it is also true that this homeostatic system evolved under conditions where humans were much more physically active than modern humans. All homeostatic systems have limits and it is plausible that at very low levels of physical activity the homeostatic system does not work so well. If this is the case, increases in physical activity from very low levels to moderate levels could have some positive effect. But, this is speculation.
Although the World Cancer Research Fund study shows that physical activity is protective against weight gain, it does not delve deeply into the mechanisms behind the protective effect. They do cite some evidence suggesting that the increased insulin sensitivity from regular physical activity may play a role. So, you certainly could be right that the positive effects of exercise on weight maintenance are not primarily due to the increased energy expenditure due to physical activity. Certainly the Church study shows that compensatory effects do exist. Whether the simple calorie in/calorie out explanation or some other explanation mediates the protective effect of exercise is an a question that probably requires further study.
I agree with the general point of the article: exercise alone will not help one lose weight. Controlling one's diet is another important factor and can often be more important than exercising. If the sole goal is weight loss, exercise may not be the most important factor (although I haven't seen any good evidence yet showing that it hurts weight loss as suggested by the article). Consistent with this view, the WCRF report cites many randomized controlled trials that show that a combination of physical activity and dietary interventions are effective at promoting weight loss.
Finally, the fact remains that strong scientific evidence demonstrates that exercise helps to maintain body weight and protects against weight gain as well as other diseases like diabetes, cancer, and heart disease. Even though regular physical activity may not promote weight loss as well as people think, there are still many good reasons to exercise regularly. Exercise may not necessarily make one thinner, but it will certainly make one healthier.