You are confusing comments with comment votes. Comment voting is disabled for controversial sites to prevent people from suppressing other opinions. You can still leave a comment for the site, but the comments are no longer ordered by votes by default. You can learn more here:
http://www.mywot.com/wiki/FAQ#Ratings_vs._comments
Edit: People are supposed to rate based on how much they trust websites. Granted, some of the rating components are not well suited for all websites.