Many people call the calorie in/calorie out equation as outmoded and flawed. And to be honest it isn't an exact equation. That's why two people can follow the same diet and have different results. For an overview of how the equation works, see this blog post.
Here are a few points to consider about using the calories in/calories out equation for weight loss:
So is a calorie in really a calorie out? No. Does using the calorie in/calorie out equation lead to weight loss? Yes. I think it's a good enough approximation of what is going on inside the body where if you use it, you'll see results most of the time. It worked for me.
Of course you want to be losing fat, not muscle, so you do have to think about that in addition to calorie counting. That's where exercise kicks in (especially resistance training).
I think the biggest (but hidden) benefit of using the calorie in/calorie out equation is that you pay more attention to what you're eating. If you're tracking what you're eating, you're typically going to eat better. I know I do on days that I track.
But tracking calories typically isn't a lifelong sustainable habit. For some it might be, but not for most (certainly not me). So the hope is once you train yourself to understand not only the portions and calories in the food you typically eat, the nutritional content, as well as how your body reacts to eating them, you won't have to continue to track. Then you're just a fit person with a good knowledge of how to eat in a healthy way on a daily basis. And that's a good place to be.