It encourages others to post more these comments.

Since comment scores was removed this is the only way to signal this to others besides the original commenter.

That said it should not be overused. If it annoys someone I guess they should downvote it but I don't think there is a need to reflexively downvote every time someone adds a friendly meta comment.

(And if people start gaming it for karma farming I guess it should be downvoted relentlessly until that stops :-)