A lot of it probably comes from deeply negative personal experiences, combined with a general propensity for people to apply a categorical belief to particular experiences. People who were treated badly by a particular group of Christians, or people who see and hear about certain Christians advocating for some terrible politician or political goal, are applying a generalized belief to how all Christians act, and potentially to all religion in general. It’s much harder to accept that the world is a deeply complicated and messy place and that religion and religious belief is a much more complex element of human civilization, culture, and personal identity than what many people would care to acknowledge.