I do keep a cover on my iPhone simply because it's impossible not to at least occasionally have to keep it in some relatively punishing environments (pants pockets, backpacks, etc), plus it's at a much higher risk of being dropped.
But for the iPad? Nah. I did usually keep my iPad 1 in the Apple case, but it was always the screen I was worried about protecting, not the back. No matter what you do, the back is inevitably going to get a scuff here and there, so there's no sense worrying too much.
It's kinda like a new car. You're completely neurotic about keeping it clean and worrying about parking lot dings, until the first time you spill a bit of Dr. Pepper on the passenger seat. Then you start to put it all in perspective and chill out about it.