First things first...are you trying to ROOT, or are you trying to flash a ROM. These are 2 different processes, and I personally get really annoyed by people who talk about them interchangebly (not to mention that if don't tell what you're trying to do, how are we supposed to help you do it?).
Short answer to your question...no. To used Autonooter, or any of the current rooting methods I'm aware of, you need an SD card that has been flashed to make it bootable. Which is why you can't use the nook, most phones/mp3 players, and some card readers. The computer has to access the sd card as a very low/high level (whichever means basic for storage card partitioning). That's not something most devices can do.
I was able to use my MP3 Player as a card reader when I ran Autonooter for my Nook. But that's probably the exception. There's really no harm in trying anything you own that plugs into a usb port, and uses a microSD card. As long as you don't let it reboot in the device, nothing bad will happen. It probably won't work, but all that happens then is you boot up the nook with the flashed card in it, and it just turns on like normal.
Or just spend the $5 on a card reader, or borrow one from somebody.