Thanks for your comment. News Genius' site is a bit misleading, as there are a few different ways one could wind up with site annotations.
The first, as you mention, is by opting in. I agree that such a tool could be a useful way to foster discourse on your content. This tool is not meant for people who opt in to Genius annotations.
Further down on Genius' page, it states that any page can be annotated simply by prepending `genius.it/` to a site URL, regardless of whether the content publisher has granted permission. Unfortunately, the comments section of any Internet page tends to showcase some extremely uncivilized discourse. This is why many site authors choose to disable comments. Genius circumvents these people's wishes. Further, unlike a comments section, Genius does not actually notify the owner of a website if his/her content is annotated. Site owners have the option to moderate comments; it took Genius until today to even add a Report Abuse button.
Hopefully this clarifies some of the motivation. Thanks for sharing your perspective!