The factual reasons are:
1. The Roman Empire was overthrown by Christianity and this is deeply engrained in history.
2. Religions force a morality on governments which they would rather not have much to do with. Any religious leaders in the past century and even in the past half century have taken the government to task, amongst them Cardinal Spellman.
3. The government knows it can't function without the allegiance of a population. Religious people tend to give their allegiance to God. The government is jealous of this divided attention.
4. Psychiatry and psychology try to bend the will of the people. Both subjects are violently atheistic and can only survive providing they can maintain a monopoly on the control of the minds of children and the population at government expense.
5. Governments fear the arising of a spiritual leader who may lead the population to resist decrees and exploitation. They therefore try to depopularize, blacken the reputation of, or assassinate any potential spiritual leader.
Religious persecution occurs at those times when a government is ruthless and oppressive and seeks total dominance of the citizenry. Since World War II, we have been trying to live with such a government.