Trivial example: it's easy to delete any file most recently accessed more than N months ago [+] with a trivial line in cron (the exact line escapes me -- it involves find), but doing that with a database requires that you roll your own access tracking logic. Incremental backups of a directory structure are easy (rsync or tarsnap); incremental backups of a database appeared to me to be highly non-trivial.
[+] Since we could re-generate PDFs or gifs from our source of truth at will (with 5~10 seconds of added latency), we deleted anything not accessed in N months to limit our hard disk usage.