They're half right. A GUI is natural, in that it embodies properties of the real world. However, those properties are not particularly simple. The reason that people find GUIs easy to use is that the human brain has evolved to function in the real world. By mimicking the real world in certain ways, a GUI can leverage the power of the human perceptual system, thus making the functionality of the application easily accessible to the user.
Reality is complex GUIs mimic aspects of the real world.
However, the real world is complex, and this makes GUIs difficult to program. Strictly speaking, a GUI is an algorithm. It accepts input and generates output. However, the input comes from a human, and is therefore very complex. The user could click and then type, or type and then move the mouse, or open one window and then close another, or insert a disk, etc., etc.