I believe it is merely a part of the tren that began in the late middle ages with the development of scientific theory, which in turn resulted in the Age of Enlightenment hundreds of years later. Now, here we are as a result. We know how the pysical word operates. We know a lot about pychology, sociology, biology, and chemistry etc. These things do a great job of explaining how things work. These explanations often conflict directly with how people have said things work using Biblical references. The two seem to contradict each other. Faced with emperical evidence and reason, the Bible seems to make little sense in this regard, and proven scientific methods seem to be most correct. So, when this happens, people think "well, if the Bible was wrong about _______, then maybe all of it is wrong." Then they abandon belief in God.
This is the result of poor understanding on both sides of the issue. Scientific inquiry ought not rule out faith in God. In my Biology 101 class, the first thing that we learned was that the feild of biology does not possess the knowledge to say anything concrete about God: this means biological science can not be used to either confirm or deny the existence of God. Biology exists to study what can be studied pysically. God can not be studied pysically. Biology, therefore, can not study God and can not make any claims about God. The study of God belongs to the realms, more or less, of metaphysics, theology, and philosophy.
In turn, feilds like theology do not possess the right to make statements about how things work. It is not up to theology to make statements on things like gravity, or molecular structures, etc. Theology is concerned with God alone.
When these two try to say one thing about the other, confusion often occurs, and the weak of faith tend to outrightly reject one or the other completely. When people look to science to explain the world and can't reconcile it with their theology, we get atheists. When people look to theology to explain the world can can't reconcile the sciences to it, we get people like Fred Phelps.
Also, many people are atheists because they see people who believe in God (this definately applies to people of any faith, Christian or not) who say one thing and do another.
On the bright side, statistically speaking, I believe there are now more Christians making up the total world population than ever before. The downside is that in predominately Christian societies; places where there historically have been populations of people whose majority were Christians, atheism is indeed on the rise; and church attendence is on the decline. These would be places like Europe, North America, and now, Central and South America. The reasons here are a little more complex and outside my scope, but I think it has a lot to do with the Enlightenment (in Europe and America), and modernization, imperialism, and capitalistic expansion into Central and South America. The more we import our material pleasures to other places that never had them, the more the people there have something else to live for than God (meaning, "hey, look at all the stuff that can make me happy now, why bother with church?")
Just my two cents.