yes, I use Calibre with the command line almost exclusively.
I was searching a way to manage my ebooks, and I was rather bewildered by the itunes / iphoto-like interface of Calibre. Let's make a comparison, for managing my photos I use digiKam, which just offer a conveniant interface to the hierarchical organisation of my folders. I store my pictures by /date/month/file-name and digikam helps me to sort files by extracting extra informations such as exif or by adding tags. Digikam doesn't move or rename my files.
I wanted to do the same with Calibre. My ebooks are sorted by /language/authorlastname-title and I wanted to keep this simple organisation, and adding a conveniant interface to this. I don't want to create an additional hierarchy with an inconvenient naming scheme. As for backups, I do backups, but I prefer to backup with the same filenames.