iTunes organises music differently to how I want it to be organised.
I also would prefer to drag/drop using explorer windows - it works perfectly well for local hard discs, removable drives, memory sticks etc, so I'll be sticking with using it, and avoiding iTunes because of this reason.
You can turn it off... or at least my Mac version allows me to turn of iTune's meddling. I initially hated iTunes meddling with my collection until I had a HDD failure awhile back and re-organised my library with iTunes from my backup drive; was easy, just select all my songs and import and it organises them neatly.