I disagree very strongly with those who interpret this movie as having having a bone to pick with religion. In my opinion, this movie is very positive about religious faith. There may be some spoilers after this point, so read on at your own peril.
In my opinion, this movie is metaphor for for issues facing the Christian church today. The two characters, Eli and Carnegie, are the only two characters in the movie who seem to be aware that the Bible still exists. One of those characters, Carnegie, wants to use the Bible to exercise power over others, because he knows its been used for that purpose in the past. That is not an anti-religious message - it is the truth - there have been many unscrupulous people throughout history who have twisted Biblical teachings to their own aggrandizement and to build their own power over others. The other character, Eli, possesses what is apparently the last Bible in existence, and he reads the Bible daily, and tries to live by its teachings, though even he acknowledges that at times he has failed to do so. Eli is on a mission of faith, he believes God spoke to him and told him to take the last Bible west, though he (Eli) doesn't know why or exactly where, and he believes that God will protect him and provide for him along the way. For 30 years Eli has walked where faith directed, never finding his destination, but everyday reading the Bible. In the end, Eli is forced to relinquish the last Bible to Carnegie, and that's when thing get interesting, for it is then revealed that the last Bible was a Braille Bible. Carnegie cannot read it, and the only person he knows who can, refuses due to the way Carnegie has treated her and her daughter. In the end, Carnegie has lost control of his town because he lost so many men in the pursuit of Eli, and is dying of gangrene. Carnegie pursuit of the Word of God did him no good because he sought to use God's Word for evil. Eli, on the other hand, carries on to Alcatraz, where a group lives who seeks to restore the lost knowledge of the past. His admission to their colony is his possession of the last King James Bible - in his head. Before dying, he recites the Bible word for word so it can be printed again. AND - we learn that Eli is blind - and apparently has been for 30 years. Throughout the movie, Eli shot animal s for food (including a flying bird with a bow), and defended himself with blade and gun, and yet was blind the entire time. Eli was protected by God, because he sought only to follow and act upon his faith. So if this movie has a bone to pick with religion, it is with false religion, with those who seek to use God's teaching for selfish and evil desires, whose with true faith are protected by God and provided for by God.
Finally, a word about the violence in this movie - yes - it is very violent, and much of the violence is shocking. However, note that throughout the movie, Eli resorts to violence on when necessary to feed himself (animals), and when necessary to defend himself. Those who offered no threat to him were not harmed by him, only those who sought to kill him, or to keep him from completing the mission which God had sent him on.