To charge your kindle, you need to connect it via usb, and the eject it. This command should work on any Kindle in any recent Linux out-of-the box. You have have to install "eject", though:
sudo eject /dev/disk/by-label/Kindle
If you don't have /dev/disk/by-label look for the first partition, e.g. /dev/sdb1 and eject that, not sdb itself.