oh no, my nook color isn't rooted and all my covers from kobo bookstore and fictionwise etc all show up.
www.monoprice.com   this is the greatest website for cables
i recommend this for all your cable needs.  Great quality and prices that are insane, ( I feel like Crazy Eddie now  LOL)
also when you connect your nook color to your computer you have to make sure the nook color is unlocked ( like when you first turn it on and swipe the unlock key)  I remember my first day with it,  I did not do that I was ready to pull the hair out my head, luckily my wife was there

  she said make sure it's unlocked.  and that was it.