I know when I rooted and had Droid Mod 1.0 there was an option to remove Car Dock too. I might grab that one Corinacakes mentioned because I never heard of it before today.
Edit: Well they want $0.99 for it - I don't use my car dock enough to really need it that bad, although that's cheap, but would like to test drive it first.
Has anyone tried Dock Blocker? Does it disable the magnet altogether? I was hoping to disable Car Home, but still allow a program like Setting Profiles to turn my bluetooth and GPS on when I dock in the car mount.