File systems are nice if you need to do manual or transparent script-based manipulations. Like 'oh hey, I just want to duplicate this entry and hand-modify it, and put these others in an archive.' Or use your OS's access control and network sharing easily with heterogeneous tools accessing the data from multiple machines. Or if you've got a lot of large blobs that aren't going to get modified in place.

What the world needs is a hybrid - database ACID/transaction semantics with the ability to cd/mv/cp file-like objects.