As far as I know, Cpanel's cpbackup-script uses plain ftp to transfer files. I think there should be an option to use more secure protocol, like SFTP or SSH to do this. If you feel the same, please vote for this enhancement in the Bugzilla:
http://bugzilla.cpanel.net/show_bug.cgi?id=4899
http://bugzilla.cpanel.net/show_bug.cgi?id=4899