There has been a creeping movement toward federal tax monies going to faith groups for "secular" purposes, which is a violation of the separation of church and state. Strings of control come with government money (rightly so), which undermines the liberty of the faith group who receives it, as well as misuses tax money paid by citizens who would not want their money going to those faith groups. For instance, I wouldn't want my tax money going to support Mormon social ministries, which extend the influence of that group as they serve the community.
What they want is for us to hold tightly to the principle of the separation of church and state -- a Baptist principle.
I know a lot of atheists. I don't know any who want to persecute people of faith. Sometimes they tease Christians, but that is hardly persecution. Christians tells all kinds of tales about atheists that are cruel and unkind. Many atheists have taken that position because of abuse within Christian churches when they still believed. When they rightly reject the abuse piled on them, they often reject the faith that they abusers claim, and see it as part of the problem.
You may want to trot out China and the USSR as examples of Christians being persecuted by atheists, but that is more a function of a political system trying to destroy anything that claims ultimate allegiance over the citizenry.
They are not claiming neutrality, they want our government to be neutral in regarding to religious convictions. They want separation of church and state to be consistently enforced.
You are equating worldviews and religious faith, they are not the same.
Yes, exactly. They want the US government to give consideration to those who are not religious when evaluating their refugee status, just like the government takes into consideration that a refugee who is Christian may well face persecution in a country where they are a religious minority. In other words, they seek equal treatment under our law. Why would you be against equal treatment for everyone under our law?