make sure you change in to the directory with WCS in it before running it (cd there first), as it will look in the current working directory
if you used some form of GUI and just double clicked to open WCS, the working directory will be your home directory so it will look in there for config.ini instead of the WCS directory
of course there is a linux beta version of WCS, although i would suggest using the latest stable one under wine for hosting with as there are bugs with the latest beta