I’ve never thought so. I’ve always thought it an incredibly incisive satire of church and especially of theological education.
In this BBC video from 1979, John Cleese and Michael Palin go nose-to-nose with some clerics, defending the movie. Decide for yourself, but I think that the guy in the pink robe with the huge pectoral cross might be doing even more to make Jesus look silly than the film. And don’t skip the end, in which John Cleese talks about his own journey in the church.