What religious message is O'Connor trying to portray in her writings? What are some of her stories in which religion the most prominent theme?

Flannery O'Connor has been called many things religious: a Christian humanist, a sacramental writer, a fundamentalist, a Yahwist, a mean Christian, and my favorite, a "Roman Catholic not like a Baptist or Methodist but like an Atheist."

In Miss O'Connor we find a devout Catholic, but her characters are evangelical Protestants; she is an orthodox who divulges no explicit theology; and she is a writer of Christian concerns who lampoons modern Christendom.

Confused?  I haven't even begun...

She writes what look like very serious short stories and novels, and they are, but REMEMBER they are comedies.  Not comedies like Shakespeare's, more like Dante's: divine comedies.

Miss O'Connor uses grotesque comedy as a humanistic leveling of luke-warm Christianity that leads her protagonists and readers indirectly to discover what is holy.

Her short stories are her best artistic works: "A Good Man is Hard to Find" is my favorite collection of her short stories, and my favorite story.  In it, she attacks her own characters as to their "once saved, always saved" self-righteousness with the Misfit--an archetypal devil.  He says:

Jesus was the only One that ever raised the dead and He shouldn't have done it. He shown everything off balance. If He did what He said, then it's nothing for you to do but thow away everything and follow Him, and if He didn't, then it's nothing for you to do but enjoy the few minutes you got left the best way you can--by killing somebody or burning down his house or doing some other meanness to him. No pleasure but meanness.

O'Connor's complete religious vision is found in her two novels.  Of the two, Wise Blood is the most accessible.  In it, Hazel Motes begins the Church of Christ Without Christ, a lampooning of the modern church is its vacuous bureaucracies and unholiness.  Her attack is upon the civil religion of the day: the watered-down Christianity that focused on self-improvement and materialism rather than salvation and the sacraments.  Her implicit solution is Jesus, not the long-haired meek surfer Jesus that adorns oil paintings, but the "soul-hungry" ape-man Jesus who hunts down Christians who try to desert Him:

He [Hazel] was going to be a preacher like his grandfather and a preacher can always do without a foot. A preacher's power is in his neck and tongue and arm. His grandfather had traveled three counties in a Ford automobile...He would climb up on the nose of it and preach from there and sometimes he would climb onto the top of it and shout down at them. They were like stones! he would shout. But Jesus had died to redeem them! Jesus was so soul-hungry that He had died, one death for all, but He would have died every soul's death for one! Did they understand that? Did they understand that for each stone soul, He would have died ten million deaths, had His arms and legs stretched on the cross and nailed ten million times for one of them?...Jesus would die ten million deaths before He would let him [Hazel] lose his soul...Jesus would never let him forget he was redeemed. What did the sinner think there was to be gained? Jesus would have him in the end!