Whenever either Christians or atheists get to a certain point in a logical examination of their beliefs, they find mystery.
For example, let's take the topic of free will.
For the Christian there are two seemingly incompatible truths:
First, that human beings have a free will and can make real decisions. You can see this throughout the Bible in every command and every bit of praise and every bit of blame. If we were mere puppets then we couldn't make real decisions - for good or for bad - so there would be no need for commands and no point in praise or blame.
Second, there is the truth that God is in control of everything, down to the last little thing.
So how do those two beliefs fit together? I don't know.
But the atheist faces a similar dilemma.
On the one hand, most atheists seem to believe that people can make real free-will decisions, otherwise, why would they write books and give lectures and otherwise try to persuade people to become atheists?
But on the other hand, athiests believe that everything is based on purely natural processes: one thing leading to another to another to another, the previous things causing the next things, from the beginning of the universe right down to their lives. But that means their decisions are not really decisions, but are just the inevitable result of preceeding events.
So, they believe in free-will and they believe that free-will is impossible, two clearly contradictory beliefs.
Okay, so what is the difference between the Christian's dilemna and the atheist's?
Well, as a Christian, what makes the seeming contradiction acceptable to me is that I know the One who understands how they fit together and who wouldn't have told us these two truths if they did not fit together. So I can reasonably assume that the logical conflict I face is resolved in dimensions or ways that I can't begin to imagine.
But the atheist - by definition - cannot appeal to God or any "higher power" who might assure him that, despite appearances, his contradictory beliefs fit together. Therefore he has no reasonable cause for believing that the logical conflict he faces can be reconciled, and he is left with nothing but contradiction.