In a time of rampant atheism its important we pray for atheists and show them love and respect and engage them in discussions as well. They are our brothers as well.
Here is a post I wrote to a Christian struggling with the concept of the bible vs science:
It is important to factor in that human perception of anything including quantum physics is not perfect and does not have to be to be useful to embrace essential truth. That's a concept we have learned to live with both in physics and in religion. So when it comes to the ancients they where teaching revelation concepts to their children the best they understood it. The book didn't fall from heaven. That by no means undermines the concept of salvation, crucifixion and resurrection which was much more observable.