The thing is I think end users are evolving. I find that the generations that grew up before pervasive computers were pervasive are the ones having the most issue with these things. When I watch my 7 year old nephew use a computer 10 times better than his parents, it makes me thing that maybe designing UI to match "real life" concepts might not work so well for future users. Desktops, folders, ... those concepts that are supposed to match real things are now becoming a hindrance and limitation on the older computer users today. Just the idea of having the same file be part of multiple folders is complicated for some users.
I think Google's label/tag metaphor for email classification is rather natural. Of course, it could get confusing when your labels are implemented using folders, such as via links.
But there's also a lot of shallow knowledge among the digital natives -- kids who've grown up in a world where there have always been computers, GUIs, Google, YouTube, or now, even Facebook and other social networks.
They know the basics, they're not afraid of them, but unless they've either been taught or are self-motivated to explore, discover, and learn, they are rote users, not informed users.
