Currently, the downvote button is only supposed to be used for unproductive comments - drivel, and the like. Of course, people use it to show their disagreement (even though that's not how it's meant to be used).
As a result, people that post controversial or minority opinions often get downvoted, even if their comments are well-thought out. This effect is less noticeable on Hacker News than on some subreddits (/r/politics is one of the worst), but it's noticeable to someone who reads Hacker News regularly.
I fear that this is going to exacerbate this effect. We can establish rules for which comments should be endorsed, just like we establish rules for which should be downvoted, but in other forums, the way that these tools are used in practice oftentimes do not match the stated guidelines.
EDIT: Also, I'm not entirely sure why this is preferable to simply allowing users to automatically hide comments below a certain score. Unless there really is a significant difference between the views of users with > 1000 karma and the rest, the "endorse" button is not fundamentally different from an upvote, is it? (In principle, not in implementation).