It's close to the same, but it's not exactly. I think part of the appeal of the Kindle is the stock OS that puts all your content right there where you want it. Once you root it and change that you may as well buy a Nexus. With the stock boot loader you have the menu bar with your music, a music player integrated into the volume control, books listed on the menu with lending library access, and the neat bookshelf design.
To each their own but I think people rooted them as has been said above, because the Nexus didn't exist. Some bought it as a Kindle, others bought it as generic hardware.
I used the Go Launcher on mine but eventually removed it. I even had second thoughts a few times and re-installed it (gotta love the cloud, Amazon just re-installs things even if it isn't carried in their store). Eventually I just removed it again and never looked back. I like how if you don't set a preference the home button was a quick change between. I just found myself never needing the other launcher. My Nexus will be here soon to tinker with and the Kindle will be my dedicated content device.