I would certainly not call Napoleon Dynamite a Christian movie.
That being said, the movie had nothing profane in it whatsoever. No cussing, no nudity, no sexual references, no homo themes nothing! Just good clean fun.
Another cool thing about the movie was it was made on a shoestring budget yet was able to bring in millions of dollars. Napoleon Dynamite sent a message to Hollywood that movies that appeal to the younger crowds do not have to be filled with sex, language or violence (no that I oppose violent movies).
Yet on the other hand it was pretty violent when uncle Rico hit Napoleon Dynamite in the face with a steak.