I am a Christian, and I'm inclined to agree. There is a certain amount of Jesus-comparison that's unavoidable, because he is a messiah-type character through and through, since he was originally conceived as a Moses metaphor, who is indeed a type of Jesus, and currently the most popular messiah is Jesus, so that comparison will continue to happen, it will always be available for commentary and analysis of the philosophies that Superman media portray.
And while it's great to use Superman to explore philosophical issues, when those views are exclusively Christian, it dilutes the actual Christian messiah, Jesus as some sort of fisticuffer, which he isn't, or Superman into a pacifist, which he also isn't. There are similar themes but there simply is not parity. If we make Superman too Christ-like, especially in the modern Catholic-inspired vision of Christ we end up with a very moody actionless Superman, like Superman Returns. No one likes that, even Christians. That's not the way to go with Superman, imho.
Those are my thoughts on the matter, with admitted bias, of course. "Hey! You got Superman in my Jesus!" "No, you got Jesus in my Superman!"