Greetings, dear Messers, and peace to you! At the outset, I would like to thank you: your question actually sets forth the logic of something I've tried to state here for years: religious people are scared of atheists; I'm not scared of atheists; therefore, I am not religious.
For those religious people who ARE afraid of atheists and who happen to be of the "christian" persuasion, I offer one word: antichrist. Other "christian" religions, while perhaps not in agreement with a particular other one... still profess Christ, in some manner. So, with the exception a few (with the WTBTS leading the pack)... they all try to get along in spite of their differences/disagreement as to doctrine(s). Atheists, however, utterly reject [the concept of/a] God and, since many of these [christians] believe God and Christ are synonymous... they believe atheists have rejected Christ (their god). Which pans out to:
"Reject God = reject Christ = an antichrist = man of lawlessness = Satan, the enemy of all those who 'believe in God'."
Thus, atheists = the "many" antichrists, who are agents of Satan, their [perceived] enemy. Given the power and kind of "evilness" these attribute to Satan (and his agents) - just look at how he is most often portrayed - these fear him. Since they fear HIM... they fear his "agents," atheists being at the top of that heap (apostates are in there, as well, but not as bad as atheists, for some).
They have all of this fear because they don't KNOW Satan (not really know him; if they did, they would know that he has no power, other than what is given to him by each person; he is impotent otherwise)... nor do they know Christ, the One they claim to have their faith in. Because if they knew THAT One, they would know that (1) all authority has been given HIM, even over Satan... (2) that One doesn't lose a single one (except the "son of destruction", who is NOT Judas; that "son" has not been revealed, yet, and we actually don't know that Judas is lost, because he hasn't had his judgment, yet, and his suicide indicates a repentance... and JAH is merciful and shows mercy to whomever He wishes to); and (3) if God is FOR them... as they like to claim... WHO, including Satan... can be against them? They would know the answer is... no one.
So, while emotion might be why they fear to the extent they do... they fear atheists... because of what they THINK they know as to who and what atheists are. Which is quite erroneous. It isn't those who claim no belief in [a] God; it is those who claim it... but are actually "false christs" and "plants"... whose purpose is to mislead, if possible, even the chosen ones.
I hope this helps.
Again, peace to you!
Servant to the Household of God, Israel, and those who go with... and a slave of Christ,
SA