Religion seems to be a constant target for criticism in the Adventures of Huckleberry Finn. Those who are religious are often painted as overzealous, and many of them are manipulated because of their faith. It seems that Twain places organized religion in opposition to his central anti-racism theme; Huck feels like he has to renounce religion in order to help Jim escape to freedom. Twain might have painted religion in such a negative way for several reasons: 1) his own personal views on religion; 2) the common belief in the antebellum Southwas that God had made black people naturally inferior, and that slavery was OK; and 3) the church was an easy target for satire. We think, most likely, it was some sort of combination of the three.
Although it prompts several of his internal moral debates, religion, with its strict policies, ultimately hinders Huck in his developing friendship with Jim.