I think that there is a lot of unexpected overlap between religion and humor. When I go to church I find myself able to focus and stay tuned into the sermon when the preacher tells a funny story, anecdote or joke. I think I understand what the video is trying to get at and I think College Humor is using humor to try and cushion a very touchy subject while still proving a point, however; I think the way they are arguing their point is weak and unpersuasive. I get that they want religious people to be more tolerant, which is sometimes true, and the comparison of drawing religious people similar nerds is funny. What I don't think is funny or persuasive is the undercutting of all religion in the process of telling people to be more tolerant and less obsessive.
On the idea that "real people" understand the points made in the video because they are less obsessive and more understanding of other's views and ideas I think it is a little absurd. I think that no one person is any more real than another. The qualifying of one person as more real than another reminds me of a scene from the TV show, 30 Rock where the executive Jack is telling some of the cast and writers of the fake show, TGS, that they need to reach out more to the "real America". Liz, the writer and creator of TGS laughs and tells Jack that no one part of the country is any more real than the other. I am coming from the same place as Liz in this situation, although I think that some people have a better grasp of reality than others, I don't think people who are more vapid or more in step with what society thinks as a whole, are any less real of a person.