Regardless of their intended purpose according to the SO FAQ, the comments in Stackoverflow are often the most interesting part of a question or answer. They do more than coordinate improvement to the attached question/answer. The comments often provide valuable context, point to other resources, and can offer some opinion.

I agree that a comment consisting of nothing more than "thank you" isn't particularly helpful, but a "thank you" + some twist or application tip is interesting and valuable. Sadly, some SO-cops just see the words "thank you", ignore the rest of comment and then immediately recite the rules and/or delete the comment.

As for SO communicating the difference, I think they already do. Their problem is that people like me _deliberately_ ignore "the rules" and post whatever we think is appropriate-- the mods just can't keep up.