Those who believe in spirits, higher powers or hold various other religious beliefs are threatened by atheists and agnostics, because both groups cannot be persuaded by personal experience.
It might be that most atheists and agnostics are not as cruel as some make them out to be, but they are perceived that way, because they deny people their personal experiences.
Many religious groups (Christianity included) are taught that people can be persuaded to convert when one tells their personal testimony (i.e Christians will share how God saved them and changed their life) or that all they need to do is quote whatever Scripture the religion abides by.
They have little idea how to present an argument to someone who deals in facts and logic, and those that do, have usually been taught untrue facts to quote to atheists and agnostics, leaving an opening for them to be torn apart by the knowledge these people have.
Since religious groups (Christianity included) do not know how to communicate with atheists and agnostics and cannot convince them they need to be saved, or that there is more to life, atheists and agnostics have been declared to be "under the influence of the devil". Meaning the devil has such a hold on them they cannot be persuaded to change their minds.
Atheist and agnostics are demonized because they hold steadfast to their beliefs and values, to the point of criticizing and belittling those who believe in God or other higher powers. Although to be honest, what religion isn't guilty criticizing or belittling other faiths and beliefs?
Atheists and agnostics are viewed as a threat to those of religious beliefs, because they disprove what churches teach, that no one can be happy without God and that morals are impossible without God.