I have looked around a bit on the web, and can not find a solution to this. As far as I know, I have the .rtorrent.rc file in the correct directory, but rtorrent refuses to acknowledge that it is there. The file wasn't automatically downloaded like it was supposed to, so I found one on the Internet and put it in my home directory. Below is a picture to where I have the file located. It's at the bottom. My username in this is tcochran.
This is the latest rtorrent, assuming apt-get is up to date... and I'm running Ubuntu Server 12.04 LTS.
So, I don't see why won't rTorrent use the file when it's in the correct location.