The plurality of belief in God/Gods. If God is just, righteous, the defender of all that is good, why allow such a massive "operation of error" go unchecked? Why not intervene? Why the suffering?
Prayer doesn't work, for anyone. All one has to do is believe, then prayer becomes "real".
I lost faith in the Bible. Adam and Eve, the Flood, Jesus referring to these are real events. It all crumbles down. There is no such thing as salvation, sin, Satan, God, etc. Life makes a lot more sense without trying to justify it with the miraculous intervention of invisible deities that are unprovable.