I think the theme will vary in the eyes of the reader. Many people saw this as an anti-Christianity story because it made attacks on the church. However, religion and church are two different things. What decisisions some people may make, good or bad, should not be reflective of all members of the church. According to the story, there were only a few involved in this corruption and those few did believe they were doing the right thing.
The idea of codes and was very interesting because it showed what facts and revelations are right under our noses that we do not even know to look for them or how to understand them. It is as though we have the power to find all the answers but we are not yet ready to do so.
I think the strongest aspect is faith. Every main character has a strong faith in this story and each feels he is in the right.