I came across a quote in Neal Stephenson's novel Snow Crash recently, which will be offensive to most Christians and also to most atheists (what fun!). It said, "Ninety-nine percent of everything that goes on in most Christian churches has nothing whatsoever to do with the actual religion. Intelligent people all notice this sooner or later, and they conclude that the entire one hundred percent is bull___, which is why atheism is connected with being intelligent in people's minds."
I think "ninety-nine percent" is hyperbole or overstatement, but the basic sentiment is true. As always, Christianity is in dire need of reformation, though many of its adherents don't seem to notice. Recently I've had a number of conversations with or about young people who are "disappointing" their very sincere parents by not following in the traditions of their faith. And it occurred to me that in these situations this difficulty only exists because the traditions they are rejecting are not even found in the Bible! If only the older generation would not invent or perpetuate "standards" that originate from man rather than the Holy Spirit, the consciences of the believing younger generation would not have to conflict with what they have been taught so often. On the other hand, parents who are careful to draw the line between what are scriptural convictions and what is mere wisdom and preference find that they share a sweet fellowship with their grown children, because the main thing is the main thing and that is what bonds them together. (I'm not saying it's easy, however...in my own case I have had to say, "I wouldn't do it that way, but he has freedom before God and I'm determined to not be legalistic about this.")
The quote above also waylays atheists, in case you didn't notice the subtle implication. The character in the novel says that intelligent people can see there is a lot wrong with "Christianity" as it is commonly practiced, so they reject the whole kitten caboodle, and thus atheism has become associated with intelligence (wrongly, because atheism only goes "halfway" toward a more thorough intellectual investigation that would reveal true biblical Christianity to be reasonable). A friend said to me recently that she discovered by reading the New Testament that Jesus was not nearly as concerned with "right-wing politics" as many of his followers are today, and so she was also questioning "the whole Son of God thing." But these are apples and oranges. The connection between Jesus and right-wing politics is not one that can be made by a careful exegesis of Scripture, but nothing is more clear on its pages than Jesus' own claim that He was the Son of God. Christians do misrepresent what the Bible says (because we are all sinners, as the Bible says), but that doesn't mean the Bible itself is wrong. That widespread leap of logic is understandable, but fallacious nonetheless.
Another example of atheism being "halfway intellectual" is Penn Jillette, who has a new book out called God, No! in which he says that atheists (shouldn't it be agnostics?) are humble and Christians are arrogant, because the latter claim to know the truth about God. "I don't know," he says, "so I'm an atheist." Well, I don't know either...so...I would need someone greater and more knowledgeable than myself to tell me what the truth is, like someone who made the universe and then condescended to communicate with us by inspiring human literature that could then be available for people of later generations to study as an objective source of truth. And therefore I am not being arrogant when I say I believe something to be true based on those books, I am actually being humble because I am admitting that I do not have the ability in myself to determine what is true. In fact, I not only am incapable of observing or comprehending enough to discover or discern truth on my own, I am very likely to misunderstand it because of my many biases. So I am utterly dependent on outside revelation and supernatural illumination. This is hardly self-aggrandizing, in fact it goes against my natural pride to admit that I am so pathetically helpless without God's grace.