In my opinion, there are two reasons : the first one is fear, fear of the unknown actually. If someone is a self proclaimed good god fearing christian, they can relate and identify themselves safely to other believers. So these people will view an atheist or an agnostic as some sort of a loose cannon, a person with no boundaries and low morals, not to be trusted. Someone they won't allow to marry their daughter...Never mind that different groups of believers don't get along so well and compete with each other!
And then, it's a form of denial caused by narrow-mindedness and intolerance. By refusing to acknowlege that someone could simply think differently, it allows believers to deny others even the right to exist and consider them as morally, spiritually and intellectually inferiors. Believers often have this attitude : "you don't know what you're missing", they consider themselves the exclusive keepers of "the truth" when actually, most often an agnostic or atheist becomes such as the result of a very educated decision and extensive research for some, the rest being plainly not interested in religion at all. Even though religion is on the decline, it is fair to say that religiously inclined people are still a majority, at least in the US, so the numbers play in their favor. That too comforts them in their self-righteousness : "so many people can't be wrong". Nobody wants to live next door to a formerly convicted felon, by essence considered an inferior person. By asociation, a number of christians will not even tolerate the idea of atheism. If one takes a moment to reflect on the number of people slaughtered in the name of religious beliefs over the centuries, the numbers will show that nobody is superior to anybody and that applies to christians and other religious goups as well. Thou shall not kill applies to everybody.