Use the following syntax to indicate a comment. Comments will not be published.
; Comment text goes here.
That is, only a semi-colon at the beginning of a line, followed by a literal space, will cause that line to be treated as a comment.
You can alternatively surround the region with the <comment> tag.
If you wish the comment to be published, but just commented out using the comment syntax of the output format, then set muse-publish-comments-p to non-nil.