My Nexus 7 also just updated to Marshmallow (6.0) and while I normally don't use calibre via USB, I thought I would investigate.
After the connection to the PC is made, look in the Notifications area (the drop-down list at from the top of the screen). In my case I saw a message
Code:
USB for charging
Touch for more options
I touched the notification and was presented with the options
Code:
Use USB for
O Charging only
O Transfer files (MTP)
O Transfer files (PTP)
O MIDI
I selected the MTP option and calibre instantly saw my device.