That's the entire point of the article, The author argues the File System metaphor is going away. It doesn't mean the File System itself will cease to exist, or that it won't be ever-present in every major operating system. What the author means is that it just won't be exposed to the end-user.
And good riddance. The File System is by far the most confusing aspect of computing to newcomers and even those that have been working with computers for a while. Understanding directory structure and the way it is organized in any given operating system seems to be a big problem for people.