When I purchased my iPad I wanted to protect it from damage so I also purchased the Apple folio style cover. As time went by I liked this arrangement less and less.
The "flocked" surface was difficult, if not impossible to clean.
It added to the weight of the iPad in my hands.
Little bits of detritus tended to accumulate around and under the edges.
It looked quite ugly, the naked iPad looks much nicer.
Now I have a simple (Gecko) sleeve for when the iPad is not in use and like this arrangement much better. As an extra precaution I place it face down (in the sleeve) on the coffee table when not in use
It does mean the the iPad is less "drop proof" while in use but I almost always use it while sitting in the lounge room. I do have memories of dropping my Newton Message Pad (and the horrid sound of shattering glass) I must admit.
The next question is whether to "use protection", for the screen that is.