I think you are being naive. They don’t like Christians, and they don’t like Christianity.
I think Cleese is on a path. I think there is a lot of stuff that annoys him about Christianity in western civilization, but that does not make him hostile to the message of Christ. But I may be projecting, because that is the way I see it, more and more, the older I get.
Remember the Holy Hand Grenade of Antioch from The Holy Grail? That was not making fun of the bible or Christ. It was making fun of organized religion that calls itself Christian. I see a LOT of that in their comedy even from the 60’s.
But they have all gotten quite a bit older and, well, people’s positions on stuff change as they become older and more educated.
However, this also true: Tho with age comes wisdom, sometimes age comes alone.