Persecution in the name of an ambiguous god is incredibly desponding. Why are social norms so easily accepted? Why is a religious belief that diminishes the virtue of another made with such conviction? If god has not made himself apparent, how can one be sure that a certain path is right or wrong, lineage being excluded as valid? Why is hatred so easily manifested toward a political, moral, or philosophical dissenter? Why do people not confide in themselves enough to see these things?
You ask some seriously difficult questions! All I can offer in response is that people 1) generally find it very difficult to overcome the beliefs that they were raised with (or that they settled upon as teenagers, possibly in philosophical rebellion), 2) often become defensive when their beliefs are challenged rather than examine their own beliefs, and 3) tend to look down on or dismiss those who do not agree with their philosophy. All of these traits make it very difficult to overcome the hurdles you mention.