1) Stories become popular despite negative sentiment in comments, or stated another way, some of the most popular stories on the front page of HN have little support in the comments. This indicates that the people who up-vote the stories in question are either not actually in support of the story's premise, or choose to remain silent in the discussion.
2) People are using up-votes as a way to bookmark stories, since that's the only flagging mechanism available to them.
The root of the first problem as I see it is that it is too easy too up-vote stories. This creates a low threshold for groups of organized users, i.e. friends of the poster, to get stories on the front page. Perhaps limiting the ability to up-vote stories in particular would have a positive impact here.
The second problem has an extremely simple solution: add a way for users to flag stories without up-voting them. Maybe a star icon that adds a story to their 'saved' directory.
Whoa... mind blown. I never noticed that feature before. Thank you Wise Weasel. (Not that I would up vote a post just to save it. but it is nice to know I have a list of all articles I've up-voted.)
+1 on having a "save" feature. However, I would shy away from using the term "flag" as a way to get something into the saved list. Flagging a post is already available and has a very different meaning.