now if you were involved the first day that root came out, i'd not advise anyone who's not familiar with command lines or using adb to try it. but now the root process has come so far that it's pretty brainless.
the only thing that requires a little thought is prepping your sd card. must make sure you pick the right drive to restore the image to. since they've found a few programs that work in windows to create the image, it's actually very easy. of course you'll end up formatting your entire card, just make sure you back up.
the auto root is so easy that all you have to is put in your sd card and... well that's it. the auto root even reboots and removes the boot files when your done so that it'll boot up from the nook instead of the sd card upon finishing root. it'll even enable market, install a multi-touch keyboard ported from the droid x, and add soft keys for back, menu, etc.
there's really nothing to lose (except your data currently on the nook's internal storage, which you can redownload if you have it backed up). you can easily unroot your nook also.
one other thing, after formatting your sd card for the root process you'll need to reformat it in the nook (or more complex ways with your computer) to reclaim the entire card. otherwise it'll only have a 40MB partition available.