An authoritarian one-party government correctly views religious organizations (or corporations, or large unions) as a threat to its power that needs to be managed.

With regard to religion, they can try to cope with this by driving people out, "reeducating" people, or manipulating the leaders of the church (issuing threats or just appointing their own Catholic bishops, Buddhist Lamas, and so on). I believe you will find examples of these things happening in modern China.