Excerpted from my upcoming book, 7 Truths that Changed the World (Baker 2012)
Theists and atheists do reason differently about God and the world. A common skeptical objection to the enterprise of Christian apologetics is that believers engage in a god-of-the-gaps form of reasoning. This charge means that the Christian theist typically attributes gaps in (especially) scientific knowledge to something God has done. For example, when science can’t explain how the universe came into being or how life originated on Earth, the Christian apologist is quick to point to God as the cause or explanation. Thus the skeptic’s accusation is that Christians do nothing more than give their ignorance a name—“God.” No real and adequate explanation, says the skeptic, is provided by simply appealing to God as a cause or source.
The atheistic naturalist (a person who believes that the physical cosmos is the ultimate reality) assumes that, given enough time, scientific exploration will discover a naturalistic explanation for whatever is now inexplicable….Ironically it might be called “naturalism-of-the-gaps” reasoning….
Regardless of the course taken by naturalists, most sophisticated Christian theists refrain from dependence on a god-of-the-gaps form of reasoning. Rather, Christian scholars tend to appeal to God as an inference to the best explanation. This form of logical reasoning resembles the way detectives, lawyers, historians, and scientists reason. For example, scientists sometimes postulate ideas that are unobservable in order to explain the data that is observed (consider for example dark matter and dark energy). This approach posits the biblical God as the best explanation for all the significant realities in life.
Christian thinkers do not naively assume divine activity or intervention as an explanation for whatever humans cannot yet explain, but rather offer a genuine explanatory theory for the nature of life’s realities. For many, inference to the best explanation (abduction) serves as the most powerful and cogent approach to explaining reality.
Reflections 
Everyone believes in God – Romans 1:20: “For since the creation of the world God’s invisible qualities–his eternal power and divine nature–have been clearly seen, being understood from what has been made, so that people are without excuse”.
So why are there people who align with atheism? To feign that they have an intellectual problem with the evidence when in truth they want independence from God; they choose separation rather then connection.
LGPE:
Scripture is clear that all people in their heart of hearts know there is a God (Rom. 1). So in a real sense from a Christian perspective unbelief does involve a moral dodge from responsibility. But I think it is better to take their questions and objections seriously and provide reasonable responses and thus attempt to persuade them than it is to accuse them of an inner hypocrisy.
Best regards.
Ken Samples