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.
I've noticed a submission might get a huge amount of upvotes yet the highest voted comment goes against the article/post submitted.
I understand there are a few things that could be going on: you can learn from bad articles/posts; those who like the article/post submitted find it unfair to downvote just because they don't agree on a contentious issue; or it becomes a what side can out-vote the other side (the one against vs. the one in favour of the submission).
Is there a commonly held view on why this happens? Sometimes I click upvote to save an article I've not read yet, not necessarily because it is a great or good article. However, I also sometimes click upvote because there is a comment inside it that I find very enlightening. Would it help at all to be able to save comments like we 'save' submitted articles? My apologies if this is too unrelated and meant to go somewhere else (email). Please let me know if this is the case. Thank you!