I recommend you read the unofficial FAQ [1] and the official guidelines [2]. In short, you can't downvote a story but you can "flag" it, which penalizes by pushing it down the page. You can downvote comments if you have atleast 500 karma.

[1]: http://jacquesmattheij.com/The+Unofficial+HN+FAQ

[2]: http://ycombinator.com/newsguidelines.html