I still haven't tested Calibre with my N7 yet, but I think the problem is due to Jellybean not support UMS (USB Mass Storage).. it only supports MTP and PTP. These are more at the software layer then hardware layer, so it's not giving you direct access to the file system, but instead it uses the MTP protocol to share content with you -- kind of like the difference between mounting a file system directly or using FTP to see the files on a file system.
I hadn't heard of either MTP or PTP until getting my N7, but this is a disappointment to say the least. I was able to get the file system mounted on my Linux system [post here
], but I've not tested this with Calibre yet to see if it's enough to make it happy. Also Calibre does not support MTP nor do they plan on supporting it [source
] so hopefully we can find a good middle ground so the N7 works with it more seamlessly.