Protestantism often leads to atheism because the Protestantism preaches about God, who does not fulfill His promises.
Jesus promised to create the church and the gates of hell shall not prevail against it. The Protestants are taught that the gates of hell prevail against it with huge success - so huge, that took its "Reformation."
Jesus promised that the church would act of the Holy Spirit who will guide it into all the truth. Protestants declared everything that was created by the church for fifteen hundred years, with the assistance of the Holy Spirit traditions and commandments of men.
Jesus Christ has entrusted with the care of the Church To the apostles led by Peter and their successors . Protestants declared that the apostolic throne was taken by Antichrist.
So, the Protestant begins to think on a subconscious level that he cannot rely on such an unreliable God. Now he is at one step from atheism.