Mark Twain (Samuel Clemens) was not a fan of “church”.  He once commented :

 “The church is always trying to get other people to reform; it might not be a bad idea to reform itself a little, by way of example."   

This attitude comes through in The Adventures of Tom Sawyer.  Religion is often presented as ridiculous in the same way that Huck and Tom’s superstitions are ridiculous.  For example,  the adults place a huge importance on going to church even though a bug is more interesting to them than the service.  In the same way, Tom’s superstition about his lost marbles is so important to him, that it shakes the “foundations”of his faith.  The difference between the superstitions and religion is that the children, particularly Tom and Huck, have no belief in the religion at all, it is merely routine to them.  On the other hand, the adults have a huge faith in the routine of the religion, not realizing that it is just like the faith of Tom and Huck in their superstitions.  By presenting the religion of the inhabitants of St. Petersburg alongside of the superstition of the boys, Twain makes a strong statement against the hypocrisy he saw permeating the church in America.