The purpose of rating comments is for quality and civility, which are independent of the article they relate to.  I agree rating for "is this a good comment" is entirely subjective, but perhaps they're using that question to derive metrics for each commenter.  See, civilcomments has an option whereby the moderator can set a given commenter's profile to "trusted commenter" which means they get to bypass the three ratings every time they post a comment.  

As for the civility rating, that's the heart of the civilcomments concept and i think it's long overdue in this forum.