While that may be true for Facebook users, it's not true for users of specific sites that use their comment system. Part of my thinking when coming up with the idea for IndexTank is that sites need to control their UX (search in our case). The vast majority cannot invest in building backend technology, so they use what's readily available and easy.

Facebook comments are easy, but they are not customizable. I haven't tried Disqus, but if I were them I'd focus on ease of use and control (not by the end user, but by the site).