iBooks doesn't come installed on iOS devices, so that's not what happens when you use the device as it comes. (You just get the ability to Quick View it.)
I think it's a little strange to have to download an application called iBooks so that you can save documents (that you need to email yourself). Apple tries to be very intuitive, but document management on iOS is a mess. There is much room for improvement. I've had multiple people ask how to get documents on their iPad, which stands out because most everything else is so simple (especially after iOS 5 not needing as much of an iTunes lifeline).
On Kindle you go to Docs and it says "Nothing here, email something to XXX@kindle.com". You try that and boom it shows up. If you want to load some documents on your iOS device there's no obvious way without getting extra apps (which itself isn't obvious). iOS 4 addressed this somewhat to allow management through iTunes, but even after plugging it in it takes knowing to go to your device in iTunes, selecting Apps, scrolling down, clicking on an App under "File Sharing", clicking the "Add" button and choosing your file (then sync and hope it works, it doesn't let you know what file types are allowed so it's a crapshoot).
It's a side effect of iOS not having a shared repository of files. I'm surprised that iCloud didn't attempt to fix this, but it only keeps application specific documents in sync. Dropbox is still king, but because they're not integrated into the OS it feels like a hack. Maybe it's coming, but right now the iCloud folder on your Mac is hidden: http://www.macstories.net/tutorials/use-mobile-documents-fol...