"In the beginning was the Word and the Word was with God and the Word was God". Jump down to verse 14 (don't have a bible out so forgive me if the reference or quote is wrong)... "And the Word became flesh and dwelt among us."
What this does not say is that "in the beginning was Jesus." It was the Word of God that through all things were made which became incarnate in Jesus of Nazareth. John is calling his reader back to the creation poem with phrases such as "In the beginning" and the "Word". ("And God said, 'Let there be...'".)
The Idea that Jesus was in the beginning with God comes by viewing the text through the lens of the trinity doctrine which wasn't around until the fourth century. It is also through the doctrine of the trinity that one would take on a literal understanding of the father/son relationship between God and Jesus.
This, however, is not what John was getting at when writing about the Word. It is much more likely that the writers of the gospels, along with Paul, were using metaphors rather than literal language.
As Marcus Borg points out in, "Meeting Jesus Again for the First Time", you could just as well substitute Sophia (as it refers to the Wisdom of God) in place of the word Logos (Word). See Proverbs 1, and Proverbs 8 to get a little bit of an understanding of this.
Borg points out that "the Sophia of God was in the beginning, active in creation, and is present in the created world". And then the sophia of God became flesh and dwelt among us. "Jesus is the incarnation of the divine Sophia, and the Sophia became flesh." (pg108).