God Before Dogma

This trope happens often in series where the main villain is The Fundamentalist, but the author doesn't want to imply that Religion Is Wrong or Belief Makes You Stupid. Instead, a sympathetic character is shown as being religious, but as rejecting the flaws of the religious villains, such as corruption or intolerance. The hero may call out the villain's restrictive or intolerant doctrines, and say that God/the gods/Cthulhu would be ashamed at what is being done in his name. Often done by The Heretic and accompanied by phrases like "Jesus wants us to love everyone."

Compare The Heretic, Turbulent Priest

Literature

 * In The City of Ember series, Nickie rejects the absurd restrictions set by Mrs. Beeson on behalf of the Prophet of Yonwood, but she still believes God is good and would honor people's differences instead of marginalizing them.
 * This happens in Madeleine L'Engle's books a lot. For example, in A Swiftly Tilting Planet the Llawcae family is devout but hates the witch-hunting Puritans like Pastor Mortmain, and Ritchie Llawcae refuses to build a scaffold to hang the 'witch' because he says Jesus would never have done so either.
 * Dorry Stevens in Leaving Fishers by Margaret Peterson Haddix, who rejects her old creepy Christian cult but still believes in God and values religion, as opposed to fellow escapee Zachary, who literally says that religion is evil.
 * Another Margaret Peterson Haddix example: Jed Reston, the son of Lord Reston, priest to the king, says state religion is all "smoke and mirrors" and has nothing to do with true faith.
 * In Chris Crutcher's novel Staying Fat for Sarah Byrnes, the liberal Rev. Ellerby is contrasted with the uptight and hypocritical Christian Mark Brittain.
 * Friar Tuck in the Robin Hood mythos is a 'good' religious foil for the villainous Bishop Hereford.
 * Aramis's devotion to God is contrasted in The Three Musketeers with the conniving Cardinal Richelieu.
 * This is a recurring theme in Katherine Kurtz's Deryni novels, because members of the Christian hierarchy claim that Deryni are evil by nature (hence justifying persecuting them), but a schism eventually occurs within the Church when some clerics, led by Cardiel and Arilan, dispute this assertion. Things get complicated when some few Deryni discover they have Healing abilities and as everyone knows Christ healed. A rebel leader who has been attacking mages' estates and tenants (particularly those of a certain Deryni duke) is forced to confront this when he gets a demonstration of Healing; Cardiel [a human bishop] is there to emphasize the contrast between the religion and some of its self-styled followers. Later, a guilt-stricken and self-hating Deryni [King Kelson's mother, Queen Jehana] has her anti-Deryni religious indoctrination overcome by Deryni clerics Arilan and Father Nivard. It's important to note that the Deryni are true believers, at least in part because of the evidence of experience. They sometimes perform rituals for powerful workings that summon beings taken to be angels (and specifically named: Raphael, Gabriel, Michael and Uriel). They mostly see coloured light and fleeting impressions of wings, and of course they could be mistaken or rationalizing their experiences, but they do believe. It also helps that their powers are triggered by an altered state of consciousness akin to meditation or prayer. Human Queen Richeldis suggests that Deryni may be above ordinary humans and just below angels on the Chain of Being.
 * Small Gods has Om discovering that his "followers" believe in the organization, hierarchs, high exquisitors, prophetic texts, rituals... anything but Om himself. Since Gods Need Prayer Badly, this means he ended up starved into near-oblivion by his own church and doesn't even have enough juice to perform the only miracle he wants now — which is, obviously, braining the guy currently responsible for this state of affairs.

Film

 * The plot of Saved
 * Dogma runs on the trope. The whole point is that following the dogma gets you into trouble, but faith is what gets you out of it. Rufus's comment that Jesus is kinda ticked off about being used to justify "Wars, slavery, televangelists", and Serendpity's comment that faith is more important than belief. Add to that the fact that even the fallen angels lampshade the fact that the rules change over time and that it's the rules set down by mankind, not God, that creates the potentially world-destroying loophole.
 * In the original version of The Wicker Man, when the protagonist, a dogmatic, virginal conservative policeman, and a young cop see graffiti spelling out "Jesus Saves," the young cop comments approvingly of it while the protagonist demands it be wiped clean.

Live-Action TV

 * In the CSI episode "Alter Boys", Grissom tells a Roman Catholic priest who suggests that he should start attending Mass again that whilst he [Grissom] believes in God, he doesn't accept the doctrine of the Church, and that too many people have died for particular interpretations of religion. Word of God confirms that this was intended as a comment on 9/11, which had recently taken place at the time the episode was made.
 * On Mad Men, when the priest tells Peggy that she should repent before nuclear war breaks out (during the Cuban Missile Crisis), Peggy answers that she can't believe God would be so cruel as to condemn her to hell just because she had an affair with a married man.

Tabletop Games
"Novalis, Archangel of Flowers: Every human religion since the first boils down to just two principles: Behave and don't hurt each other."
 * Called out several times in In Nomine, where religions are mostly seen as a "human thing," given to mankind as a way to approach the God that the angels already know to worship. Even the few Archangels that explicitly prefer a particular religion (Catholicism for Laurence and Dominic, Islam for Khalid and Zadkiel) still acknowledge that worthy contributions can be made by those of other faiths. By contrast, the Demon Prince of Factions, Malphas, loves fine points of dogma.

Web Comics
"T-O-E: There is some powerful mystery between all of these perfect, solid things... and that is my God. My God is what I don't know."
 * In Rice Boy, The One Electronic rejects the "perfect, solid God" that he was taught about as a child, and believes that the being who sent him on his quest to find The Chosen One is not God but an imposter. But T-O-E still believes in God.

Web Original

 * Mr. Deity is appalled by the contents of the Bible.