As I've said in several other posts, if you don't use your Kindle 3 with the cover on (as I prefer), just blank the screen with the power switch before putting it into the cover. I've never had a problem when doing that.
I don't like using it with the cover because it doubles the weight and is more awkward, and can't easily be used with one hand while in the cover.
One of the major attraction to the Kindle is it's light weight. Using it in the cover voids much of that advantage for me.