I'm pretty sure this was their point, that stating it as simply "calories in calories out" makes it sound a lot easier than it actually is in practice.
I could buy that, except that the clear implication was that diets don't work because of the language. The article plainly blamed the use of the phrase "calories in, calories out" as a major factor in why diets don't work. That's just not true, the caloric equation isn't why diets don't work, the caloric equation is precisely why diets do work. The phrase also is not the reason that people don't stick to diets either. Sticking to a reduced calorie diet is fighting our instincts and our habits and behaviors and social circles, not our language.
Diets "work" the same way the war on drugs is "working". You just have to wrap your hands around your eyes and stare really hard at the details, while being very careful not to see the bigger picture.