Reading testimonies of former members of Bible-based cults and abusive churches and considering my own experience, I noticed that these groups often cause people to lose their faith in God. I think the main reason for that is authoritarian leadership in these groups.
On the one hand, the leaders present themselves as appointed by God and carrying out His will. They make their followers believe that they have unquestioned highest spiritual authority and this authority is given directly by God. Leaders also make members of their groups believe that they have a special commission from God and carry out His will on the earth. Everything they do is presented to the members as God's will. On the other hand, these leaders abuse their authority. They make people suffer constantly and severely. However, members of these groups are expected to believe that all these sufferings are directly from God. This causes them to conclude that God is very cruel and wants people only to suffer. This concept hinders them from seeing God's love and care for people.
I have read somewhere that there are two reasons why people deny God. The first reason is because they do not have adequate information about God. Nobody preached the gospel to them. They just do not know who God is. The second reason is when people have some reasons to feel that it would be better if God did not exist. I think this is exactly the problem of former members of abusive and mind controlling groups. They think that God is very cruel and subconsciously feel that it would be better if such a God did not exist. This leads them to losing faith.
The solution of this problem as I see it is for the ex-members to change their concept of God. I think reading the Bible and healthy spiritual literature may help them to see God in a different way. After I left the group where I was, I spent much time on studying the Bible and Christian theology. It really helped me to see God in absolutely different way. I realized that the concept of God taught in that group was completely wrong.
God does not want people to suffer, though He sometimes allow sufferings. There is a difference between what God really wants and what He allows to happen. The Bible, especially, the New Testament is full of God's love to people. Christ had to suffer crucifixion in order to save people. This was a great price paid for us, and this was a great manifestation of God's love.
The concept that God is cruel and wants people to suffer is not biblical. God is different from the concepts of cults and abusive churches.