Modernity is a war of religious ideas, not a war on them.
In his fascinating book, The Soul of Doubt, Dominic Erdozain demonstrates that it is not science but conscience that has produced our modern culture of religious doubt. “The ‘religious roots’ that I consider fundamental to modern cultures of unbelief are twofold: the positive content of dissent, including conscience, Bible and Christian ethics, and the negative stimulus of dogma, persecution, and theologically induced fear.” (7)
Beginning with the Reformation, Erdozain makes a case that Martin Luther was the prophet of conscience and an early leader during the time when orthodoxy would become the measure of a Christian. A conflict between conscience and creed will begin that will run into the modern era.
Other players in this drama include Calvin, Thomas Muntzer and Sebastian Franck, Sebastian Castellio and Baruch de Spinoza, Voltaire and Pierre Bayle, Charles Darwin and T. H. Huxley, Ludwig Feuerbach and Karl Marx. The focus is on how religious faith can lead to doubt when the orthodox, theologians especially, do not live up to their moral convictions. Preaching about a God of love and then killing other Christians in wars of religion for example, caused philosophers to question theology.
Although doubt and uncertainty existed before Luther’s time, Erdozain begins his study with the Reformer. Luther fought for the freedom of his conscience when disputing the Roman Catholic Church. An older Luther railed against the Jews and went from an attitude towards people who didn’t agree with him as “differing brothers” to “heretics”. Though Luther abhorred the religious wars, unfortunately his orthodoxy “was preparing the ground for a policy of persecution.” (26)
Reacting to this, Muntzer, Franck, Castellio, and other “rational Spiritualists” developed a theology of love mixed with a faith that existed in the inner person. It was deep in the soul and was demonstrated as “obedience to an already resident light.” (64) Erdozain asserts that this grounding of reason in the mystical conscience “did not anticipate the Enlightenment; They made it happen.” (34)
Moving right along to Spinoza, Erdozain, who said, “Spinoza was a ‘born again’ believer.” (90) explained that the thrust of Spinoza’s Ethics is “the power of the enlightened mind to break out of the tyranny of the passions.” (116) Many were rejecting what they saw as the cruelty in the doctrine of predestination. Erdozain’s claim is that Spinoza was not trying to destroy the Christian faith, but to rescue it.
I’d like to pause here and discuss a thread throughout these centuries – the “inner light” of not only Spinoza, but the English Levellers and the Quakers and Madame Jeanne Guyon and the Dutch Collegiant Christians. Erdozain’s discussion of inner verses outer authority is still relevant today. Do we know from within or without? Is there a Holy Spirit? Does He speak to us? How can we know? Is there a sensing of truth that cannot be explained by secular materialism (Taylor)? I believe that knowledge is both. It is not either/or but both/and.
Continuing with Voltaire, Erdozain pressed his claim that Voltaire also was a Christian thinker who was not attacking Christianity but orthodoxy. He hated clericalism and sought a “theology of mercy to complete a lively but ultimately barren doctrine of conscience.” (121) Moral reason, or conscience, should not be seen in competition with intellectual reason, or science. For Voltaire as for other “doubters” it was the inconsistencies in the Christian religion – persecution, slavery, and other injustices that made them question Christian orthodoxy.
Moving into the nineteenth century, Erdozain argues that the crises of faith are ones of conscience. The Victorian conscience was more theological than scholars realized. He says that “science and religion came to live in relative harmony in the nineteenth century, arguing that the warfare of science and religion was actually part of the wider revolt of conscience against religious authority. As in the Enlightenment: conscience and science can be distinguished but not separated.” (175)
It was not science, Erdozain says, but disenchantment with the Bible and orthodoxy. Erdozain quoted Beatrice Webb’s reflection that “with most people it is the sense of what is morally untrue which first shakes your faith in Christianity; it is moral disapprobation of some of its dogmas which forces you to question rationally the rest.” 
In other words, the doubts and/or dilemmas in the conscience are already there. People were already angry with a dogma of hell and condemnation. Now they would question the rest of the Bible or orthodoxy.
Erdozain cemented the idea of ‘righteous’ doubt with a section on George Eliot. “Eliot’s loss of faith was the classic revolt of conscience against creed.” (212). Eliot’s critique seems to speak for many when she says that dogma has the capacity to smother charity and basic intellectual honesty. I would agree that it has the capacity to smother charity, but I pray that with the encouragement of so many voices for justice, churches would re-examine the Bible and remember that Jesus did not say that His disciples would be known by their theology but “By this all men will know that you are My disciples if you have love for one another” (John 13:35)
Erdozain mentions the Fundamentalists. Fundamentalists exasperated the controversies by drawing lines in the sand and labeling anybody who did not agree with them a heretic. I think Jesus must weep when He sees the strong dividing lines we have created. Looking back for me, I think that if only ‘orthodox’ Christians would have sat down with ‘doubters’ and had open dialogues maybe both could have learned something.
Years ago I took a survey course in philosophy and when we got to Soren Kierkegaard we had a long discussion on ‘doubt’. The class was divided as to whether or not Kierkegaard was a Christian. The professor (and many including me) took the position that just because you have doubts it doesn’t mean you are not a Christian. It just means that like Abraham you are courageous enough to (respectfully) question God.
I enjoyed reading my old notes and found another interesting perspective on why people reject Christianity. Soren Kierkegaard (according to the professor) said:
People try to persuade us that the objections against Christianity spring from doubt. That is a complete misunderstanding. The objections against Christianity spring from insubordination, the dislike of obedience, rebellion against all authority. As a result, people have hitherto been beating the air in their struggle against objections, because they have fought intellectually with doubt instead of fighting morally with rebellion.
Dominic Erdozain speaks to our day. A lot of people are not turned off to Christianity; they conscientiously object to the Fundamentalist version of it. Jesus is still the answer, but let us listen to the other person before we share about Him. Are they sincerely searching for answers? Let’s don’t draw a line as the men who produced the Nashville Statement did, declaring that anyone who disagreed with them is not a Biblical Christian. I’m on the side of the doubters with that one!
 Dominic Erdozain. The Soul of Doubt. New York, NY: Oxford University Press, 2016. 261.
 Beatrice Webb. My Apprenticeship. Harmondsworth: Penguin Books, 1938. 124. Quoted in Erdozain. 210.