The nexus runs android 4 (Ice Cream Sandwich). From what I understand, as of android 3 (honeycomb) google removed the ability to mount any memory, internal or sd card, as a disk. Because of this change, calibre will not detect any device running android 3 or later.
Your choices include:
- Create a folder on your PC that mirrors the books folder on your device. Use calibre's connect to folder to maintain books in this mirror. Use a replicator (if any works with MTP connections) to sync this folder with the phone. Puresync (http://www.jumpingbytes.com/en/puresync.html) claims to be able to sync "some MTP devices".
- Similar to above, but use dropbox or some equivalent to sync the folders over the air.
- Try something like ptpdrive, which can mount some MTP devices as drives. I have no idea if it works with an android phone.
- Use the content server to access your library over the air. You might use OPDS if your reader app supports it.