yeah, I was mostly ok with the anti-religious aspect because it came across as tolerant of history's ignorance, in a sort of "you can't blame people for not understanding" kinda way which I didn't mind. I personally think that science and religion can overlap without one having to try to disprove the other. The problem that usually comes up is when those in the scientific community use history against their perceived opponents as a straw man to defend modern topics that may still be debatable. Its similar to that argument that goes something like: "50 years ago people were racist and now realize they were wrong so today you have to accept homosexuality as normal or else you're as bad as those racists." But instead its: "400 years ago the catholic church thought the earth was flat and the sun revolved around the pope; so if your pro-life or pro-family you're just as dumb as they were." Again, I think Cosmos handles this fairly tactfully, although, while that sentiment is not stated, it is easily inferred and I think purposely so.
Anyway, it was the episode on lead that really turned me off. That's when the show stopped being about the cosmos and showed its hand; that it had an agenda. They used the case of history's "science deniers" and their acceptance of lead as a safe chemical as an allegory for the global warming debate. Evil companies lobbying against the undeniable scientific truth; showing that the populace was ignorant and on the wrong side. The implication, though not implicitly stated, is that if you doubt global warming, you're on the wrong side of history just like those lead-loving dopes of the early 20th century. (and just like 16th century church for that matter.)
edit: but I heard Fargo is really good. my father-in-law was visiting last weekend and he couldn't stop talking about it.