I'm glad there's a separate thread for focusing more on religion as it appears (or maybe doesn't) in "Cosmos". But I wish it hadn't been called ".... vs.Cosmos" Because I don't think that's where they're going with this. I don't think Cosmos is an attack on religion (specifically, on Christianity).
If it is, at times, pointing out the incompatibility of scientific discoveries, principles, theories with some Christian beliefs, I think (1) It's been pretty mild in doing it and (2) to me, it's been pretty much "Here are some differences; you decide". Excuse the phrase, but imo "Cosmos" is not "preachy". The topics seem chosen for reasons other than debunking Christianity, although I'm sure getting people to question their beliefs--whether religion, or that we actually see a horizon--in the context of what they understand about science, is one of the purposes..
And re "Religion" itself, I'm no expert, but I think there are various "religions" that wouldn't have any problem being reconciled with everything that has been said on this show--and with all the concepts/knowledge we have about science. I think it is intended to get viewers thinking and questioning more. I like the humbling part of it, where you realize that some scientist observed the same thing you have but s/he actually got some scientific principle from what he observed. The whole methodology of scientific discovery is so different from religious discovery (thinking of the "big names" in religions), but I do wish he'd do even more with the scientific method.