One episode set in an alternate universive showed a world where Christianity never existed and was "advanced" (just imagine the uproar if the episode had a world without Islam that showed the World Trade Centre intact)
The Christians in the show are portryaed in a bad light either as luantics or hypocrite. The episode where Peter's father was portrayed as a fanatical Catholic because he wanted the baby baptized or the episode where Lois was portrayed as a bigot for being against gay marriage and of course the episode where it was discovered Brian was an atheist. In which Christians were shown as illogical, bigoted and Brian was hounded for his atheism.
Maybe I am reading to much into it