Additionally, there's a soft limit to how negative you can be in the comments, where you can be downvoted. Submissions can only be flagged, not downvoted, and if you flag more than two submissions a day, your flag button is disabled. (It looks like it still works, but your flags no longer affect the ranking of a submission)
Love it or hate it, it's the new self-promotion/branding via blogging. If a controversial article makes it to the top of a popular or niche internet forum like HN, and you have something of substance to say about it, it's infinitely better to post your thoughts on your own blog instead of in the comments of the social news submission.
The niche forum sees it, and you can claim credit in the comments, associating your handle with your blog. But more people may see it - potential clients, employees, funders, cofounders, employees, etc - and it's good way of beating writer's block and adding content to your professional blog.