I think it's a philosophical difference. iTunes is more database driven (which I really liked at the time for music). Let it control your filesystem, drop in your files and it'll load from metadata. Any changes will only modify iTunes' DB. Use iTunes to decide what to sync to devices.

A lot of people were super annoyed coming from WinAmp. They organized their library by filename and the metadata was often a mess. They also wanted to treat iPods as USB drive and drop files on there.

Plex is even different in that it only looks at the filename and pulls metadata from the Internet.