First, look into history more--there are several non-hierarchical (read: flat) file systems out there.
Second, while the workflow might mirror authoring more closely (which I think is horsehit, but that's neither here nor there) the artifacts of that process are what matter. Existing notions of a "file" map very cleanly onto the storage and organization of such artifacts.
There is an argument to be made for having better querying capabilities or permissions or whatever, but what is to be gained from throwing a commonly-accepted idiom away?
For instance if we throw away certain programming features from a language, we can gain reliability and security which threaten even the integrity of code that doesn't itself use those features.