Maybe it's because nothing related to files is showing up. For example, Java has packages, classes, protocols (interfaces), methods, and documentation. All of these are visualized in a Java IDE. But Java _also_ has folders and files, so these need to be visualized, as well.

At least in Java there's a pretty clear mapping from packages and classes to folders and files. In PHP, the mapping is not so clear.

Edit: I'm not saying I agree with the author, I'm just pointing out one aspect.