I wish there were more discussion venues where the quality of your participation was based on the value to the discussion, not as to whether or not you supported what that person said.
People seek social groups that make them feel good and avoid ones that make them feel insecure. They especially avoid places where they are made to feel stupid. So they tend to prefer places where their beliefs are confirmed and maybe they can get away with calling someone else stupid.
What you are fighting is as natural as water flowing downhill: animals seeking comfort. You have to overwhelm gravity itself to turn the flow uphill.
There is no lack of good discussion venues. There are only too few people who prefer them. How can any such venue attract the masses out of their comfortable, partisan clubhouses?
A great, very recent, example of this was reddit making /r/TwoXChromosomes, a subreddit dedicated to women's issues, a default sub (meaning everyone, even non-users, are automatically subscribed). The stereotype demographic for reddit is young white males. I have no way of actually verifying these demographics--I'm not sure they do either.
Yesterday, a comic about the casual sexual harassment caused by men was posted[1] and although there was some valuable discussion, most of it was pretty awful to read (the further down you scroll, the worse it gets). Although we'd like to believe that engaging in debate / conversation / dialogue generally cause us to have empathy for and understand the other side, the opposite tends to happen, especially in large, anonymous communities. And this is in a venue where the quality of participation IS (supposedly) based on the value of the discussion.
Although I think you're right that most websites (Hacker News included) suffer from only having up and / or down votes. It's possible that a more complex system might be more useful. Maybe in addition to the like / dislike paradigm, it might be useful to add quality / not quality functionality.
[1] http://www.reddit.com/r/TwoXChromosomes/comments/2d85wt/next...
Historically you lived in a place which - through economics and upbringing - was full of people who were a lot like you. You worked in a job where your colleagues were - through reasons of education and geography - a lot like you. Where you found people disagreeable generally you'd avoid them if you had the chance. You chose the newspaper you liked and the news show you felt most comfortable with on TV or radio.
We've always put ourselves in information bubbles, this isn't anything to do with the internet, the internet is merely recreating what we already had. The only difference is that with the internet it's a larger wasted opportunity because there is so much more information out there you might subject yourself to.