Yeah when my wife and I bought ours a couple of weeks ago the guy behind the counter told her, after she told him we were rooting them, that he certainly supports that because he knew people who had and loved them.
B&N knows it is selling to rooters at a high volume I imagine and they see those $$$. For me and my wife it is just stock rooted, and so the result is we have a tablet we like and she has a digital subscription to National Geographic because we actually like the B&N Nook functions built into it! We get what we want and still give B&N what they wanted out of the deal, and I think a lot of "novice rooters" like us are doing the exact same thing, really.