Of course, Pictures Under Glass interfaces have advantages too. Touching a screen has become a familiar way to interact with technology: a more tactile interface might be harder to learn. To make a screen-based interface, you only need to draw a 2D picture and respond to 2D touches, not design a 3D object which can be manipulated in space. You can buy touch panels off the shelf instead of having to manufacture expensive custom 3D parts.
But these are advantages of easiness and cheapness, not quality. If designers and engineers can put in the time to make a physical interface and users can put in the time to learn it, you can improve quite a bit on Pictures Under Glass. Think about how terrible it would be to replace a car's steering wheel with a touch screen, for example.
So that's really what the article is saying: we should think of touch screens as the cheap, easy option, not the exciting, futuristic one. Our futuristic starship control panel should be a custom-manufactured physical interface instead of a cheap glass panel.