I put my original Apple cover on my new Ipad 3 to protect when I stuck it in my Rickshaw Ipad bag to protect it temporarily. I was only gone about an hour and a half but when I got home the back of the Ipad was so warm it was almost too uncomfortable to hold or sit in my lap---when I took it out of the cover. For anyone unfamiliar with that cover it is a rubbery substance and completely covers the Ipad, front and back.
I used the Ipad all evening uncovered and it stayed cool except for a very light warmth in lower right. I decided to put it in my Propup (which sadly is too large to hold it securely) and it too is made of a light plastic form that is rubbery. It totally enclosed the back of the Ipad and it heated up again. Perhaps this is why Apple didn't use a similar cover for Ipad two with its stronger processor which may have generated some heat if enclosed and used the front cover instead.
Sitting on my lap its cool as can be but I'm going to put it in a Targus Vuescape cover----but it will be open to the air when I'm using it I assume.