I agree that on the face of it down voting for disagreement is frustrating, though I have a hard time squaring that with the understandable desire to up-vote for agreement. I think most people know when they're making a potentially contentious comment, and in that case (just like in real life), should take far more effort in crafting their comment to be incredibly fair and charitable (while acknowledging disagreement) to those who might disagree. For one it makes it much more likely for those who don't agree to read the comment charitably themselves, it's more likely to lead to constructive discussion
and have the benefit of being more immune to down votes purely on disagreement.
Edit: Looks like the two of us have discussed this before :)
https://news.ycombinator.com/item?id=12974834
And both times I've appreciated the civil discussion. Thanks for that!