The problem is reflected on both sides and primarily because of Modernity and even more specific, Kant. The atheist is trying to come from an entirely logical, intellectual position. That is their entire foundation. You won’t change their mind because they are already convinced that your argument, no matter how well reasoned or logically articulated, is ultimately based on non-reason, i.e. faith and emotion, which, to them, is a foundation of sand.
From the Church’s perspective a large part of the Church has bought into the Modern reductionist bifurcation that faith and reason are seperate. Kant seperated upper story faith and emotion from the lower story intellect and reason.
Many twentieth century apologists went full force to take this on—C. S. Lewis, Francis Schaeffer, Josh McDowell, to name a few of the more prominent, popular apologists. There were and are many more (Nancy Pearcey comes to mind right off the bat as a contemporary).
The problem is often, not only is the atheist worldview bifurcated, but so is the Christian’s. In reality the problem has nothing to do with atheists. The problem is what Christians believe vs how we live. When what we teach and believe isn’t reflected in how we live, we, ourselves, come up with all sorts of irrational, unreasonable justifications, “God’s ways are not our ways”, “The devil made me do it”, etc. Why would an atheist believe us that God is rational?
Francis Shcaeffer’s big crisis of faith was based on how much of how we live as Christians does not reflect what we believe or at least say we believe. If that shakes Christians, how would it not also shake a non-Christian’s faith in Christians? This caused him to totally dismantle what he believed and reassemble it.
The problem the atheist has is that we have given them no reason to believe our faith is rational and reasonable. Until we do that, no argument will make a difference. And that is also why Christians will doubt and maybe even lose their faith. When we can reconcile the intellect with faith, that is where a difference is made, not in arguing.
Solve that and there won’t be any reason to debate an atheist.
That’s what I think. Maybe I’m wrong, but I don’t think so.