The answer to the question why people are upset about religion has to do much with perception depending the spiritual, emotional and educational level of the individuals. Many are upset because they perceive religion as a "tool" used for controlling the masses to the benefit of the people in power; others about their representatives that don't practice what they preach; others when they see all kinds of injustices being done at all levels when the representatives of the different religions remain silent, condone such practices, profit from them, etc.; others are upset because they see many perpetrators of hideous things always get away with them while just, honest, spiritually advance people go through hell. Have run into many people expressing those thoughts and similar others in my life.