I don't have scratches on the black part of my phone, from the dock. Are you sure that's what its from? I have been using the dock for about a month now, and charging every other or every second day.
Mine isn't scratched really, but it looks like it's been rubbed there. I don't think it's from the apple dock though. I have a belkin dock that I use one of the ipod inserts for and that's what i think it is from. In the apple dock, my ipod feels kind've loose in it.
The demo iPhones in the local Apple store are all scratched/rubbed raw at the bottom from going in and out of the docks 100 times a day. So it does happen if you're not moderately careful.