I had the same problem after upgrading to Fedora 8. Somehow my /root/.bashrc was renamed to /root/.bashrc.rpmsave and my .bash_profile was gone. Here's how I fixed it:
# mv /root/.bashrc.rpmsave /root/.bashrc
# cp /etc/skel/.bash_profile /root
By the way to disable direct root login through ssh set the variable "PermitRootLogin: no" in /etc/ssh/sshd_config.