"[Comedy is] no longer... just an irreverent and humorous dismantling. As religious explanations fall further and further behind the evolution of society, comedians have stepped in to fill the gap. Comedians are the new preachers, comedy clubs are their churches, and the audience members that understands it are the frustrated moral progressives." -- a previous post on comedy (Read full here).
Whether I explicitly stated it in that post or not, I don't think comedians like Louis C.K. are intentionally trying to manipulate public opinion. They're being genuine. They're creating jokes that a majority of their audience will appreciate. It's why Louis C.K. gets away with misrepresenting atheists in the video below. He's preaching to the choir. The choir that matters to him, anyway. The average awareness level of most people is why his routine was a good thing and why most atheists, from what I've read, are happy with last week's performance. It pushed the status quo.
Since writing the above references post, I've been able to watch Bill Burr and Doug Stanhope live. These guys are even better in person than on their specials! Their personalities and beliefs show in side-comments and responses to hecklers that are edited out for video. It was a joy listening to Bill Burr and the hush that fell over the audience as he criticized an idiotic marine in the Chicago Theater. The point being not just comedy, but a critique of mindless reverence towards people who have served in the military-- a critique of "the military card". Anyway, here is Louis C.K. on SNL in case you missed it.