While I'd say it's a rare occurrence, I've definitely noticed an increasing trend of comments being downvoted by people who simply disagree. It happens in some threads more than others... Just try voicing a contrarian opinion in a thread about privacy, for example. It also happens more often in non-startup-related and non-programming-related threads.
I think a solution, if one were to be implemented, would be requiring people to specify why they are downvoting a comment. Or better yet, to choose from a list, as long as it doesn't include "I disagree" as an option. At best, it would prevent irrational downvotes. At worst, it would at least allow people to see why they're being downvoted and learn from it.