One of the more common atheist arguments against the Cosmological Argument for God's existence has been that we cannot use reason in trying to prove the existence of God given that physics has constantly been 'proving' theorems that are counter-intuitive and go against the brain's rationalistic ways of conceptualizing the world. At most, reason can only be restricted to analyzing certain elements of the natural world, but we cannot use it in determining the nature of the universe's beginning or anything beyond our material universe.
Now most of this argument (which I only offered a brief summary of) is taken from Kant's arguments on the limits of reason when it comes to delivering us to important truths about reality. Anyways, this argument has been taken apart quite a number of times in sophisticated and academic treatments of the subject, however I feel that they have been quite complex for the layman to understand (although I have an undergraduate degree in philosophy, I still find myself scratching my head at times when reading this stuff).
Luckily, I came across one of Dr. William Lane Craig's posts on the subject where he refutes the Atheist/Kantian attack on reason's ability to attain truths about (metaphysical) reality in a simple, brief and easy-to-read fashion for lay readers.
For this fun and interesting read, please see The Limits of Reason
Enjoy the read!