Why did Darwin's theory of natural selection challenge the ideas of the church?

Answer 1

Many churches of the time posited that god created all the organisms of earth at one time, so that no organism was related except to vary from it's created kind. Darwin showed that through the process of natural selection new species were constantly arising from related organisms.

Answer 2

Theism rationalizes its beliefs in deities by pointing to the organized nature of nature, claiming that such complexities could not have come about through unguided natural processes. Darwin, with his theory of natural selection, provided just that: an explanation for natural complexities in terms of unguided processes. Basically, while Darwin's theory does not claim that no gods are involved in nature, it did away with the need for any gods to explain the diversity of life.