Files are important because they act as an interface (in the OO sense) to all of the different things that the author of this article talks about. The universality of that interface is, for now, key to interoperability.

I don't care how many times david pogue says otherwise, it's a lot easier to drag the audio files i want on my mp3 player from one window to another than to wrestle with itunes. Not only is it easier, but it's a skill I can apply again and again and again to lots of different tasks. If you do want to wrestle with some kind of crazy-ass music management system, the way that seems to work best to make it so that we can all use whatever we want is to have an underlying interface based on files.

Beyond interoperability, tech that's too specific to 'what people actually use their computers for' tends to make it harder to do things that the developers didn't think of; go far enough down that road and computers become about as interesting as TVs.