His reliance on humor and absurdity allows him freedom to prune and moderate extreme arguments without attacking the philosophical premises on which they are based. This extends not only to the Catholic church, but even to his political affiliations. His reputation as a liberal comes directly from his heavy focus on republican 'absurdity', but I have watched many of his shows and have never seen him criticize conservative values. Contrast from Jon Stewart, who has actively favored the democratic party over the republican party, Colbert could just as easily be a secret republican, whipping into shape the party of his preference in defense of its long-term survival.
He's an intelligent liberal that can poke fun at both sides.
But most importantly, he's a very moderate Catholic. He doesn't do much in terms of the religion, he only considers himself one and I believe goes to church occasionally.
Moderate religious people are usually religious by tradition, they were born into it so are comfortable staying so.
The only real difference between him and an atheist is that he still believes in a god. He's not irrational except for that one thing.
Mr. Colbert shows the foolishness of Catholicism with every religious discussion by stating the pure Catholic stance vigorously.
He takes out the idea and states it VERY clearly so that every one can see how stupid it is.
His VERY point is that Catholics are NOT logical at all, ever
While I strongly believe that Catholicism is completely compatible with critical thought, I do not believe that Stephen Colbert is a good example. While I do not believe that anyone can comment on his state of belief, he has never come across as one whom I would call a devout Catholic.