First is to install rTorrent and screen if you don't already have them:
~$ sudo apt-get install rtorrent screen
Once installed, you'll want to setup your rtorrent settings and ensure they work as expected before continuing (read more).
Next comes the upstart job script. Here's what I use:
description "ncurses BitTorrent client based on LibTorrent"
start on (local-filesystems and net-device-up and runlevel )
stop on runlevel 
pre-start exec su user -c "mkdir -p .rtorrent/session"
su user -c "screen -d -m -S rtorrent rtorrent"
Replace each instance of user with your Ubuntu username. Save to /etc/init/rtorrent.conf and you're done. rTorrent should automatically start on subsequent system startups.
Update: Changed upstart script to automatically create session folder if it doesn't exist.
Viewing rTorrent's status
Since rTorrent is running in a detached screen process, you can view what's going on and basically use rTorrent by attaching to the process:
~$ screen -r rtorrent
To detach again, press Ctrl-a followed by d.
That's it . Enjoy!