Primarily it is because we understand that Jesus is the incarnation of the one God. Thus we don't end up with a second God, we still have just the one God who has made himself known by revealing himself in a new way.
One might then reasonably ask:
Why, if Jesus is God, does he then pray to God, or cry out to God for help?
or
How, if Jesus is God, can God remain sovereign and infinite while trapped in a finite human body?
or
What happens, if Jesus is God, to God when Jesus supposedly dies on the cross?
Well, first, I don't actually have to be able to answer any of those question for me to know that it is still true. The scriptures tell us that Jesus is God. If we trust the scriptures to speak truth, then we know it is true even if we don't understand the how or why of it all?
Second, I need to continually remind myself that it was not later generations of the church that said that Jesus was God, it was the disciples themselves who declared this to be so in their sermons, in their teaching, in their telling the story of the Jesus that they had known, eaten with, walked with, and in some cases, even seen crucified and then raised again from the dead. This understanding has been key to defining who and what Christians were while Paul was yet still simply another Jew intent on stamping out this new movement in its infancy before they even had been given given the name "Christian" because of what they taught about the Christ.
Third, this experience of the early church (pre-Pauline) was that Jesus was both Lord and God, the holy One of Israel, one being with the Father. They had not yet articulated concepts like the Trinity; they were still looking for words to describe it. But they knew, out of their own experience, that it was true; assumedly based on the resurrection and the presence of God flooding their lives in a new way in the person of the Holy Spirit as well. Thus, the early church would do two things: (1) they would proclaim this simple message of God in Christ and (2) they would look for better words and ways to express this understanding. Over time those words would come, big fancy words like "hypostatic union" and "perichoresis", words that were brand new then but have become common place today like "trinity".
These were not things that they took lightly. After all, they were all Jews. Jews who were passionate about the great texts of their faith: "Hear, O Israel: The LORD our God, the LORD is one." And yet, they knew this Jesus to be God. They had been listening when he was examined while on trial in the Sanhedrin and they had asked him, "Are you then the Son of God?" He replied, "You are right in saying I am" (Luke 22:70). They had seen him do things that could only be done by the power of God and they had heard him claim things, like forgiving sins, that were reserved to God alone to claim (Luke 5:17-26).
But it was the resurrection that sealed the deal. It lead Thomas to call him not just Lord, but also God (John 20:28), and Jesus blessed him for it. It lead Peter and Stephen and others to preach this message about a new way that God was dealing with humanity, through the cross of Christ and that salvation could be found no other place than in his name.
To those, such as modern day Muslims, and Jews from that old Pharisee Paul to the present day, or to anyone else who can only conceive of God in a narrowly defined box, the idea of lifting up Jesus as being this very same God is blasphemous. But it is what we believe, and that is why we have no problem worshipping Jesus, because in doing so we understand that we are worshipping the same God as before, the one God who created heaven and earth has also walked among us and died for fallen humanity. Whatever name you may know him by: Yahweh, Allah, the great I AM, his name is also Jesus. He is one and the same.
It is not shirk, for we declare no partners, what we declare is that he is great enough to be both present and invisible, human and infinite, Father and Son (and Holy Spirit) all at the same time and still be just one.