There is no "downvote" for main stories but there is a "flag" option to flag articles that you think don't belong to the HN main page. Users with enough karmas can see the "flag" option.
Ah. I thought the flag was to signal it was inappropriate so I only used it on stories like that. But I don't want to signal it shouldn't be on the main page; just that I personally don't like it: downvote would be more appropriate?