There are a lot of issues with the upvote/downvote concept:
1. It favors people who are more careless with their votes. If pro-Coke users only downvote poor comments and upvote well crafted ones regardless of beverage choice, and pro-Pepsi users downvote any pro-Coke comment and upvote any pro-Pepsi one, you're going to have pro-Pepsi comments at the top and pro-Coke comments at the bottom. The better behaved group is going to have less of an impact.
2. It favors people who skim and read carelessly. If you're reading the original article, if you're taking time to fully read someone's comments, if you're taking time to see who they are reply to and the context, your voting output is going to be less than someone who quickly skims things and carelessly throws out upvotes and downvotes.
3. It favors individuals that spend all their time online over ones that have a more balanced life. There is simply going to be more votes coming from terminally online people. This is particularly an issue in cases where you have to pass the filter of people who vote on new submissions in order to get to the front page.
4. It favors group think. There are a lot of people who think that a top comment must have some validity, and that a downvoted comment must have some problem with it.
5. It can give people a skewed idea of where the community stands. Even if everyone in the community had an equal impact on things, a 45%-55% split in the community could still leave someone with the impression that one view is completely supported in the community while another is almost universally rejected.
They don't. As the earlier points indicate, a small minority drives the conversation, and posting habits outside of the upvote/downvote system play a huge roll as well.