Threaded commenting can be quite challenging/unintuitive to grasp for non-technical users. The problem isn't that it's difficult to implement, it's an issue of UX. It might be fine on HN or reddit, which skew young and tech-savvy, but it's definitely not OK on Facebook. My parents would be lost if faced with threaded comments.
This is actually one of the design decisions behind discourse.org - its hotly contested for much of the same reasoning. Expert users 'get' threads quickly, and cant even begin to put themselves in the shoes of an internet newbie.