Authentication might seem a trivial matter, but it isn't. If you use facebook connect, your users are actually facebook's users. Facebook knows how many times they used your service, when, and so on. And, most importantly of all, you are locked in into facebook's service.
What if one day FB starts to push more and more FB connect applications to become FB apps? How much leverage would they have?
As a counter example, I use google analytics on my websites. This means that google knows everything about my stats. But if I stop trusting them, for any reason, it would take just 5 minutes to change. This doesn't give any leverage on me. Contrast this to using FB connect - or the google equivalent, for that matter.
That's what makes many independent developers scared of this kind of news... that being assimilated by FB could one day become inevitable.