I am guessing that this is an mtp problem. I don't have a Nexus but I do have a Samsung Galaxy S3. The problem arises that when you plug in a USB lead and try to view files you can only see the folders - no files. I am guessing that this is the problem you are experiencing.
I would have suggested that you used the go-mtp method, that has proved very successful for me. So, instead you could try the application 'gMTP', from the Ubuntu Software Centre. I had some success with it. It takes a while to operate so be patient when you connect your phone. Start the application first and see what happens.
I wasn't sure what to make of your comment 'when Ubuntu is running on the Nexus 7'. If you are running Ubuntu on the Nexus 7 then, presumably, there is a possibility that the problem you are alluding to might be solved with the forthcoming Ubuntu Phone image for the Nexus in February?
FORGOT TO MENTION: Airdroid - check that out on Google Play and get access to your files via a browser.
Here's a copy of my Tomboy note using the go-mtp method. It may prove useful if it differs from what you have tried previously.
sudo chmod a+r /etc/fuse.conf
sudo gedit /etc/fuse.conf
nano /etc/fuse.conf
Set to:-
user_allow_other
sudo apt-get install libmtp-dev git golang
mkdir /tmp/go
export GOPATH=/tmp/go
go get github.com/hanwen/go-mtpfs
sudo mv /tmp/go/bin/go-mtpfs /usr/local/sbin/go-mtpfs
sudo chmod a+x /usr/local/sbin/go-mtpfs
sudo mkdir /media/s3
sudo chmod 777 /media/s3
(you can change permissions later - just to make sure don't get a permissions problem)
This bit is not really necessary because the info can be gleaned from http://chakra.sourceforge.net/ccr/packages/ud/udev-android-rules/udev-android-rules/51-android.rules
Need to get some information about the phone. Can get by starting:-
udevadm monitor --environment --udev
Now plug in phone for a few seconds, then unplug.
Copy down info.
From:
http://chakra.sourceforge.net/ccr/packages/ud/udev-android-rules/udev-android-rules/51-android.rules
Get the following:-
SUBSYSTEM=="usb", ATTR{idVendor}=="04e8", ATTR{idProduct}=="6601", SYMLINK+="android_adb"
SUBSYSTEM=="usb", ATTR{idVendor}=="04e8", ATTR{idProduct}=="685d", MODE="0660"
SUBSYSTEM=="usb", ATTR{idVendor}=="04e8", ATTR{idProduct}=="68c3", MODE="0660"
SUBSYSTEM=="usb", ATTR{idVendor}=="04e8", ATTR{idProduct}=="6866", SYMLINK+="libmtp-%k", ENV{ID_MTP_DEVICE}="1", ENV{ID_MEDIA_PLAYER}="1"
Then add to it :- (replace 'brian' with user login)
Google SAMSUNG_Android MTP mode : automatic mount when plugged (all android versions)
ENV{ID_MODEL}=="SAMSUNG_Android", ENV{ID_MODEL_ID}=="6860", ACTION=="add", RUN+="/usr/bin/sudo -u brian /usr/local/sbin/go-mtpfs -allow-other=true /media/s3"
Google SAMSUNG_Android MTP mode : automatic unmount when unplugged (all android versions)
ENV{ID_MODEL}=="SAMSUNG_Android", ENV{ID_MODEL_ID}=="6860", ACTION=="remove", RUN+="/bin/umount /media/s3"
Paste all the above into:-
/etc/udev/rules.d/99-android.rules
Now restart udev
sudo service udev restart
http://askubuntu.com/questions/237664/transfer-data-from-ubuntu-desktop-pc-to-ubuntu-nexus-7-tablet-without-otg-ca
http://askubuntu.com/questions/216246/ubuntu-nexus-7-as-usb-device-does-not-work
– silentrunner Jan 21 '13 at 08:26