Why? Hierarchies seem like a natural fit for the human mind. We can know only the relevant parts, which might change according to what we're working on and confidently exclude entire large complex branches like the contents of C:\Windows or some program's temporary working files or whatever from our awareness.
They also combine in an obvious way. If you mount another filesystem somewhere, it's contained in that somewhere, not mixed in with the existing one in some unexpected complex way.
They're not a natural fit for real world data, but there's a tradeoff between serving humans and serving nature.
> Hierarchies seem like a natural fit for the human mind
I'd argue they only seem that way because we've been raised and taught to use them but haven't been taught sufficiently to think about other ways to organize knowledge.
> They're not a natural fit for real world data
In "A City is not a Tree"[1], Christopher Alexander discusses the semilattice in relation to city planning and human societies. Clay Shirky has previously noted[2] that categories and ontologies are too brittle to serve human thinking.
As an example of an ongoing attempt to create a hierarchical ontology that isn't helpful, look at any list of music genres. Also note that social networks are not organized hierarchically – humans have the ability to handle interconnected structures just fine.
This also relates to why many people don't understand or can't quite relate to true distributed peer-to-peer computing or systems where there is no central controller or fail to grasp emergent behavior. But nature is fine with completely decentralized systems: see, for example, foraging ants. See, for example, Emergence: The Connected Lives of Ants, Brains, Cities, and Software by Steven Johnson
They also combine in an obvious way. If you mount another filesystem somewhere, it's contained in that somewhere, not mixed in with the existing one in some unexpected complex way.
They're not a natural fit for real world data, but there's a tradeoff between serving humans and serving nature.