Can't think of a single good reason why anyone would prefer a folder-based organizing system to having well-tagged songs in iTunes library.
iTunes even stores all the songs of the library in a folder system like this /Music/iTunes/iTunes Music/[artist]/[album]/[song-file] (based on the info on the ID3-tags), so if you reeeally want your folder-based organizing system, it's there even if you use iTunes...
I, personally, can't live without iTunes. The spotlight-like search in the top right especially rules. It's so easy to find the albums by certain artists. I can write "apoc metalli" in there and it instantly shows songs by Apocalyptica from the album "Plays Metallica By Four Cellos" and it won't show my metallica songs.
The only thing that can be painful is if your current id3-tags are irregular/lacking/nonexistant.