With a title like "The Big Bang Theory," it is only natural that CBS's sitcom about a group of scientists would occasionally touch on religion and the origin of life as we know it. As we all are aware, religion can be a touchy subject, and when handled improperly, can result in more than a little backlash for any show that chooses to use it as fodder for any story line, but for jokes in particular. That this show seems to have avoided such a fallout thus far is perhaps a testament to how well written and well thought out each episode must be. Another reason why they might have escaped getting called on the carpet for religion-based humor is the over all tact with which they have handled each line, and the lack of maliciousness in their jokes.
Then again, it may just be down to the simple fact that they don't only discuss one religion. It feels less like someone is poking fun when they treat everyone equally as far as religion is concerned; "The Big Bang Theory" has made everyone fair game for a humorous take on their beliefs. In previous seasons the show has touched on Howard Wolowitz's Judaism in dozens of episodes and in many ways, from his mother being unhappy with his non-Jewish girlfriend to Penny mentioning his only keeping kosher on major holidays. The Hinduism practiced by Raj has also come up many times, with references to the various gods of Hinduism and other mentions. Buddha has also been mentioned on occasion, though many would argue that is not technically a religion.
In general, atheism and Christianity only seem to have come up when Sheldon Cooper's mother is either visiting or is for some reason being discussed, such as when Sheldon recalls some childhood memory involving church. However, when they do come up, they are often discussed at more length than the one liners usually devoted to Judaism and Hinduism. Still, the writers seem to have the characters discuss both sides with an equal hand, allowing Sheldon to mock his mother's faith, yet also allowing each of his friends to pray in a church as if they accept at least the possibility that someone might be listening. In the latest episode featuring Sheldon Cooper's mother, the show actually touched on Judaism, Hinduism, Protestantism, Catholicism and atheism at various times, which lent it an overall feeling of even-handedness that kept the show from feeling preachy.