We threw out the baby with the bathwater. In the west now, there is a religious vacuum, and it is being filled by people of a new religion (yes, Islam is a new religion. It is just about the finest of the Christian heresies.)
Some will say that reason has triumphed over faith in the west. You have to have a lot of faith in reason to make a statement like that. Reason has become the new dominant religion in the west, and when it is confronted by beliefs (or pathologies) which seem unreasonable, there is a clash.