Some problems with this post:
1. Is there anything beyond your opinion to substantiate your claim that children are "born atheists"? Since the majority of atheists - it would seem - tend to be naturalists and claim empiricism as the basis of reality and understanding, I would think you'd have more than just your opinion (since we Christians get dinged for our opinions about the nature of reality that can't be scientifically proven).
2. According to the Bible, all men are born with an innate knowledge of their Creator (sorry - don't have a specific text handy - apologies for that); unfortunately, sin clouds that knowledge and that is why we teach our children about God and why we read the Bible - so that that innate encoding makes more sense.
3. The idea that children left to simply question will not believe is fallacious for a number of reasons; first, a childish view of the world would seem to indicate that the sun revolves around the earth and that at night it sinks into the ocean (if you live on the west coast). Second, depending upon whom the child questions, the answers will be different (and often equally subjective). If you teach a child that the world possesses only a material existence, then yes - the child will grow up unbelieving. If you teach the child that matter is not the full frame of reality, well, the outcome might be a bit different.
4. Many of the questions asked by children and adults alike are unanswerable by science or naturalism.
Atheism is not a "natural" condition - it is a chosen condition. The greatest strivings of philosophers, artists, musicians and writers have always been to seek after the greater purposes of life, to fathom the mysteries of existence, to identify that restless longing of the heart. All those things point to something larger than ourselves, prompting us to find that thing which lies outside of us. If atheism were "natural" - well, I doubt that history would be littered with the overhwhelming evidence that all people have believed in something larger than themselves through which they and the universe take a greater, more profound meaning.



