Elie’s main thought throughout the train ride is the inhumane treatment of the people by the Nazis. Also he realizes that when people are treated like animals, then they will act like animals. His thoughts are also on God.
When he realizes that the Jews are being killed without any mercy. For example, babies are being burned in a crematorium. He cannot believe the depths of human depravity. He also cannot believe that God would allow this as well. Why all this evil? Why would the God of Jews allow this to happen? Why does he not put an end to all of this? There is confusion and anger.
This feeling is compounded by the prayers of some people, who were praying to God. They had faith, when his was weakening by the day. There were others who were even thanking God! He could not believe this. It was completely foreign to him. For the rest of the work, Elie would question God.