Colbert has some very nasty things to say against cryonics, and to people who don't celebrate Christmas.
I don't recall seeing his comments on these particular topics but it can be hard to tell when you are seeing the character Stephen Colbert speaking and when you are getting a glimpse of his actual opinions. Generally if he is explicitly attacking something it is the character speaking.
I'm not holding him up as a pillar of rationality anyway, just saying he seems more rational than Stewart (which is no great achievement in my opinion). I also get the impression that he has more scientists on his show and his questions reveal a greater understanding than Stewart's even when they are explicitly critical. This may say more about his writers than it does about him personally but his guest selection at least suggests to me that he has more of a genuine interest in science than Stewart.
I think it is true that there is a tension between being funny and giving the audience what they want to hear and actually exploring complex ideas. I don't think either program is immune from that. I should also say that I think Stewart actually does a better job than most 'real' news shows in the US so judged against the spectacularly low bar of mainstream TV broadcast journalism in the US he can actually look quite rational.
He doesn't have to be your hero.
You apparently don't see the rationality that I do. Maybe I watch more often, or maybe I'm applying Thomas's suggestion more than you.
I am curious as to your current motive. Are you attempting to say that Jon Stewart should not be a hero? That he should not be associated with rationality at all? That you don't like the Daily Show? That people in "the media" aren't and can't be rational? Or that I'm plain wrong that Jon Stewart can be a representative of the search for truth, fact, and understanding?
Light reading about 'Rationalist Heroes'.
I am not sure how useful people find having personal heroes. I would argue that they are definitely useful for children. Perhaps I haven't really grown up enough yet (growing up without a father possibly contributed), but I like to have some people in my head I label as "I wonder what would X think about this". Many times they've set me straight through their ideas. Other times I've had to reprimand them, though unfortunately they never get the memo.
One living example is Charlie Munger.
He was an early practical adopter of the cognitive biases framework, and moreover he clearly put it into context of "something to protect":
"not understanding human misjudgment was reducing my ability to help everything I loved"
(The quote is from his talk on "Misjudgment" which is worth reading on its own http://vinvesting.com/docs/munger/human_misjudgement.html)
One interesting point is that Charlie is seemingly a Christian. I have a deep suspicion that he believes that religion is valuable, for the time, as a payload delivering mechanism.
“Economic systems work better when there’s an extreme reliability ethos. And the traditional way to get a reliability ethos, at least in past generations in America, was through religion. The religions instilled guilt. … And this guilt, derived from religion, has been a huge driver of a reliability ethos, which has been very helpful to economic outcomes for man.”
Also, judge for yourself from his recommended reading list - looks like something out of an Atheist's Bookshelf.