Every computer system that uses tagging is a counterexample. We humans think in tagging as often as we think in hierarchies, but I agree that we tend to think of hierarchies as more well-defined and organized. This tendency can be incorrect.
I think it boils down to this: for hierarchical data, use hierarchies. I believe that files on a modern personal computer will almost certainly not be hierarchical, so it's not ideal to store them hierarchically. Videos, for example, may be movies, tv shows, screencasts, music videos, etc. Videos may also be standard definition, 720p, 1080p, etc. It's difficult to say, for example, which attribute should be the root directory for your videos, since it's reasonable to want to browse by many different attributes. A hierarchy does not apply to videos, but attributes could easily be represented by tags.
I think it boils down to this: for hierarchical data, use hierarchies. I believe that files on a modern personal computer will almost certainly not be hierarchical, so it's not ideal to store them hierarchically. Videos, for example, may be movies, tv shows, screencasts, music videos, etc. Videos may also be standard definition, 720p, 1080p, etc. It's difficult to say, for example, which attribute should be the root directory for your videos, since it's reasonable to want to browse by many different attributes. A hierarchy does not apply to videos, but attributes could easily be represented by tags.