A very casual look at the original text tells us that the two words translated as “God” in that text are not identical. The first one is a noun (Yeon) referring to the Father, and the other is an adjective (Yeov) which refers to Jesus. You can tell the difference between the two by looking at the last letter of the two words. It is for this reason that many translations render the verse in a way that recognizes this fact. For example, translations by James Moffatt, Hugh J. Schonfield and Edgar Goodspeed render it:

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".....and the Word was divine."

Other variations also exist. 

Today's English Version reads, "....and he was the same as God." 

The Revised English Bible reads:  "....and what God was, the Word was."

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As you can see, different translations give it a meaning in harmony with the original.  Therefore, this text is telling us that the Word (Christ), is divine just like the Father (possessing the 'God-nature').  It does not tell us that Christ is God the Father, one and the same person.

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It is interesting to note that the word “the” exists in the Greek text but was left out by translators.  Who knows what they were thinking, but it has a purpose and is important.  The phrase, “the God” identifies the one true and living God the Father in this verse.  While Jesus is called God in this verse, there is a clear distinction between Him, and “the” God whom He is with. The God whom Jesus was with is “the” God the Father.  Jesus was not the same God He was with, but instead is God in the sense of being divine just like His Father, from being the only begotten Son.  Jesus inherited the characteristics of His Father.  The Father is God and so His Son is God by nature. 

 

Just as any human by inheritance possesses the very nature and form of humanity.  Lets use Adam and Eve as an example with the same grammatical word structure.  “In the beginning was the woman, and the woman was with the human, and the woman was human.”

 

Adam is “the human” and the woman is Eve.  But Eve is also human by nature but Eve is not “the human” in identity.  They are two separate persons.

 

Another way to look at this is, “In the beginning was the Word, and the Word was with the Deity, and the Word was Deity.”  The Word, (Jesus, Son of God) was with the supreme Deity, the Father, and the Word was Deity in nature. But the Son is not “the Deity”.  The Son was not “the” Father, yet the Son has the Father’s divine nature by inheritance.  The Word has the same God quality, the same divine nature and the same God-ness as the Father.

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Many people use John 1:1 to say that Christ has always been and had no beginning.  But that is not what the verse says.  God had no beginning and has always existed.  Also the phrase or group of words utilized in the text “the Word was WITH” has to mean something.  The Word was “with” God.  They cannot be the same being, otherwise one could not be with the other. 

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However, the question that we need to address is what "beginning" is this text talking about?

Was this the beginning of earth?  Was it the beginning of creation?  The answer is No.  Whichever beginning you place it at, it has to be the beginning of something. Please note that creation is not mentioned in the verse at all.  That comes in verse 3.  "All things were made by him; and without him was not any thing made that was made."

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Thus, if all things were made by him (Christ, the Word) then the beginning in verse 1 must be before creation.  Our parallel text is found in Proverbs 8:22-30.  This passage is divided in 2 parts.  The first part talks about the birth of Christ in heaven before anything was created.  While the second part tells us who was with God during the creation.

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"The LORD possessed me in the beginning of his way, before his works of old.  I was set up from everlasting, from the beginning, or ever the earth was.  When there were no depths, I was brought forth when there were no fountains abounding with water.  Before the mountains were settled, before the hills was I brought forth: While as yet he had not made the earth, nor the fields, nor the highest part of the dust of the world." v22-26

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Christ was possessed / set up / brought forth in the beginning of God's ways.  Colossians 1:15 puts it this way, "Who is the image of the invisible God, the firstborn of every creature."

This beginning was "before his works of old", before "the earth was", "when there was no depths", "when there were no fountains", "before the mountains were settled, before the hills", "While as yet he had not made the earth...etc."  Christ is saying that He was brought forth in the beginning before these creative acts.

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The second part of the passage in Proverbs 8 says:
“When he prepared the heavens, I was there: when he set a compass upon the face of the depth: When he established the clouds above: when he strengthened the fountains of the deep: When he gave to the sea his decree, that the waters should not pass his commandment: when he appointed the foundations of the earth: Then I was by him, as one brought up with him: and I was daily his delight, rejoicing always before him;” v27-30
 

This section tells us that Christ, the Word, was with God during the creation. The RSV renders v30 this way “then I was beside him, like a master workman; and I was daily his delight, rejoicing before him always,” which brings out the point that Jesus was a workman in the creation of the world, or as John 1:3 puts it “All things were made by him; and without him was not any thing made that was made.”
 

Colossians 1: 16, 17 says the same thing, “For by him were all things created, that are in heaven, and that are in earth, visible and invisible, whether they be thrones, or dominions, or principalities, or powers: all things were created by him, and for him: And he is before all things, and by him all things consist.”

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God is the great source of all things.  And it was from him that creation was taking place thru Christ. “God….created all things by Jesus Christ”.  – Ephesians 3:9

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"God....spoken unto us by his Son, whom he hath appointed heir of all things, by whom also he made the worlds;" - Hebrews 1:1-2

 

“Who hath ascended up into heaven, or descended? who hath gathered the wind in his fists? who hath bound the waters in a garment? who hath established all the ends of the earth? what is his name, and what is his son’s name, if thou canst tell?”  - Proverbs 30:4

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These verses attribute the work of creation to two beings:  A Father and a Son.

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What we have shared here is the divine Son-ship of Christ.  And that is what John 1:1 is sharing as well.