I'm having a lot of problems with Nexus 7 Toolkit. On my new 32GB Nexus 7 I've got USB debugging checked. I'm connected to my Windows 7 PC as "Media Device MTP" (my only other choices is Camera PTP). I can get to Fastboot no problem. When I start Nexus 7 Toolkit my device is recognized and a serial number is generated. I've unlocked my bootloader (during boot up the Google logo now shows an unlocked padlock). But when I try to get it to root it goes through several steps and several restarts until it generates the following error messages: "adbd cannot run as root in production builds", "error: protocol fault (no status)", then the daemon starts successfully and I get "failed to copy root\su to system/bin/su : read-only file system" and "failed to copy root\superuser.apk to system/app/superuser.apk : read-only file system", then finally two "unable to chmod" error messages about those two actions.
I assume that all of this stems from one problem but I can't figure out what it is. Help?