In order to flatten the normally steep learning curve associated with software, there seems to be a tendency to make it fit some existing metaphor. The most common is paper; we also have cute little yellow file folders, among other things.
They succeed in their initial goals sometimes -- like the AppleMacintosh. Sometimes they fail miserably (insert your own example here). But what they (almost) all have in common is that you are not really dealing with the object that was the inspiration of the metaphor, but a crude simulation. Sooner or later, the metaphor breaks down; you can only take it so far.
To avoid this, software may have to be written so that the user has to LearnAnewMetaphor.
(An aside: when I start talking about the paper metaphor I can't help but think about the XanaduProject. It's only fitting that I link to it here.)