Filesystems have a property that changes preserve locality. A change made to one branch of the tree doesn't affect other branches (except for links). Databases lack this property: any UPDATE or DELETE can potentially affect any row depending on the condition. This makes them powerful but also scary. I don't want that every time I delete a file it potentially does a rm -rf / if I mistype the query.

The best compromise is what modern OSs have: a tree-like structure to store files but a database index on top for queries.