1) They were difficult to manage. You never know when someone is going to spam you or take a swipe at you. And if a post goes viral, you’re basically inviting both of those things.
2) Disqus, the primary comment system I used, had advertising that you had to pay for to remove, and I was going in a different direction with my ad strategy at the time. (Also, even if I was OK with running ads like that, they were no longer worth the price of admission. There was a time back when I ran my old site, ShortFormBlog, where Disqus ads brought in a couple of hundred bucks a month. No longer.)
3) There are many other venues for people to offer their take on a piece; why limit them?
I think Boing Boing’s approach of replacing comments with a forum struck a good balance.