Religion needs a way to keep its members thinking about it. If it doesn't, the religion will die. One way to keep people thinking about the religion, thus keeping the religion alive, is to have them go to war against some group of people. Psychologically, what this does is it makes the members invested. If they do these things that would otherwise be attrocities, then they must stick with the religion to make sure that they have the moral high ground. "I killed this man, which would normally make me a murderer, but since God told me to do it, this is OK." If God is not real, then it is not OK and the person thinking this would be a murderer. This makes the murderer hold tight to their beliefs so that they can stay morally correct.

It doesn't always have to be quite that extreme, but if religious members can be brought to do bad or even embarrasing things on just about any level, then they'll want to stay with the religion to justify their actions.

Defining this "other" to target for war is an important step to make sure you don't harm too many of your own religion's followers. You try to pick something that the majority of the followers do not do, that way they aren't discouraged from the religion due to liking something against the doctrine, but you need a large or powerful enough group to last a while, otherwise you'll just have to do this again in 5 minutes. Nationality is a common way to do this, just say that whatever nearby nation needs to be destroyed and you've got it.

But there are also bonus points if you can choose some group that you or your followers don't like. For example, people who do something "icky" or otherwise weird. One might say, if people do something rather queer by your standards? Homosexuality was an easy choice because we're a spread out minority that will be hard to squash because we're everywhere, most religious (well, most of any group) people are not homosexual and have little to no experience with homosexuals or homosexuality, and bias can easily be inserted to mark it as "icky" for that bonus hatred.

Now you've got your followers oppressing a group and doing horrible things ranging from rude remarks to first degree murder. The goal was never to get rid of us, we were just an easy scapegoat to keep the sheep in line all the way in ancient times.

They hate us only because they were told to by their cult leaders and the leaders only care because they need to keep their sheeple doing awful and immoral things so that they gain a psychological reliance on their faith to prevent insanity setting in as they realize what attrocities they've committed in the name of a false god. They're obsessed with us because we fight back, and we gain support. We defy them by refusing to die out so we make a good, long lasting target. If they were to kill all of us, they would likely move on to foreigners or people of whatever random race each religion chooses.