"Calories in vs calories out" is not wrong. It's just a small part of a much bigger picture.
If you go into a caloric deficit your body will give a hormonal response. This response determines if your body will start using your fat reserves, your muscles or will just shut down. This hormonal response is dependent not only on how much you eat, but also on what you eat.
Eating a diet low in carbs enables your body to use up stored fat more easily and will leave you less hungry then a low fat diet. This makes it MUCH easier to stick to your diet.