I keep it mostly in the original iPad box so the back of it is not exposed that much and sure as heck am not taking my iPad outside the house until I got a protective case. As for the logo, protecting it is not really a concern.
Really the only sure way to keep it from getting scratched is to leave it in the box at all times. In fact, if you were to take the plastic off the box, or even if there were just a small hole in the plastic, there would be good chance that a single particle of dust would get into the box, work it's way to the Apple logo (since the logo faces down if the box is upright, gravity will do this [perhaps you should place the box face down]) and scratch the logo.
Really the only sure way to keep *your* iPad from getting scratched is to not buy one in the first place