Grow a thinker. You won't always be around to sort out the fairy tales.
You should definitely stress skepticism and not believing everything at face value. To hear a person, understand them, but not adopt their ideals until you can either verify or disprove it. This of course is going to cause problems with his future teachers, but will encourage his curiosity and growth. Best of luck to you!
Tell your son the truth that there is a God. Let him read books about Jesus & the great book the bible.
The bibles New Testament is a great book, as Jesus only speaks the truth. "THE TRUTH SHALL SET YOU FREE"
Give the kid a chance to make up his own mind, he just may see the light that you didnt see. I will pray for you.
"The bibles New Testament is a great book" .. oh really?
Something like this maybe? ..
And Cain talked with Abel his brother: and it came to pass, when they were in the field, that Cain rose up against Abel his brother, and slew him.
And the LORD said, I will destroy man whom I have created from the face of the earth; both man, and beast, and the creeping thing, and the fowls of the air; for it repenteth me that I have made them.
And the LORD plagued Pharaoh and his house with great plagues because of Sarai Abram's wife.
But his wife looked back from behind him, and she became a pillar of salt.
And he said, Take now thy son, thine only son Isaac, whom thou lovest, and get thee into the land of Moriah; and offer him there for a burnt offering upon one of the mountains which I will tell thee of.
And he that smiteth his father, or his mother, shall be surely put to death.
etc, etc, et bleeding cetera.
Some book you've god there fella. Sure, give that to a five year old.
Which is lovely, only Jesus didn't write the Bible. Ever played the game of "Telephone"? The one where one individual chooses a phrase, then whispers it into the ear of the next person, who does the same, and so on? At the end, the original phrase has often been twisted into a completely unrecognizable version of itself, and all ever-so-innocently. That's your Good Book, my friend. Although, you're right: guiding a child through the reading of the Bible, or stories about Jesus (along with Zeus, the Buddha, the Prophet Mohammed, Hindu gods, etc.) is an excellent way to give them a good foundation on religion.