Agreed. For example trees of source code seem to fit the hierarchical structure very well, because it can (almost) map directly to projects, modules, submodules and classes, and conveniently separate them from e.g. build products or configuration files. Trees are not evil, but they are not the holy grail of file management either.
From a historical point of view, a traditional filesystem with a database layer on top seems to be the most logical way to go. Personally, I think it would be interesting to see what would happen if someone did it the other way around: create a whole new way of organizing files that doesn't use trees, and allow layering some kind of 'tree view' on top of that.
If not for a specific few lines of code explicitly forbidding hard linked directories, all of the modern file systems would actually be directional graphs.
From a historical point of view, a traditional filesystem with a database layer on top seems to be the most logical way to go. Personally, I think it would be interesting to see what would happen if someone did it the other way around: create a whole new way of organizing files that doesn't use trees, and allow layering some kind of 'tree view' on top of that.