Unsurprisingly, being a science program and not one of the hundreds of opposed-viewpoints-yelling-at-each-other shows that masquerade as informative TV, Cosmos has garnered criticism from religious fundamentalists in soiled lab coats. Mother Jones' piece on them is entitled "Science Deniers Are Freaking Out About 'Cosmos'" and it puts the objectors into two categories: evolution deniers and climate science deniers. (The article lists three categories, but the Big Bang deniers all seem to be creationists.)
As with Cosmos itself, the MJ article doesn't say anything I didn't already know. Intelligent design, aka creationism, is still unscientific bullshit, not to put too fine a point on it. If you don't already know why, see my 19 October 2010 piece on the subject; I'm tired of repeating myself. As for climate science, the overwhelming majority of actual climate scientists accept that the preponderance of evidence points to human activity having had (and continuing to have) a significant effect on the earth's climate. Climate science deniers generally think climate change is a conspiracy to take away the right to burn fossil fuels, so the deniers are either industry shills or those frightened by change.
Evolution and climate change (not to mention the Big Bang) are the shorthand names for our best explanations of certain aspects of reality. The explanations — aka theories — aren't perfect and no one claims they are; like all scientific theories, they're subject to revision based on better data and/or cleverer interpretations. Deniers, though, can't even offer competitive alternatives, much less better ones. I pity deniers. But their ideas are drivel and it would be irresponsible to pretend they're worth serious consideration.