The overwhelming majority of Christians believe that Jesus was the Son of God spiritually, bodily, and every other way. We believe that he was conceived miraculously within the virgin Mary by the power of the Spirit of God, and so God is his father not in only a figurative sense, but concretely. Most Christian groups consider this to be a fundamental doctrine of the Christian faith.
Jesus said he is the Son of God.
Luke 22:66-71 (NASB) When it was day, the Council of elders of the people assembled, both chief priests and scribes, and they led Him away to their council chamber, saying, “If You are the Christ, tell us.” But He said to them, “If I tell you, you will not believe; and if I ask a question, you will not answer. But from now on the Son of Man will be seated at the right hand of the power of God.” And they all said, “Are You the Son of God, then?” And He said to them, “Yes, I am.” Then they said, “What further need do we have of testimony? For we have heard it ourselves from His own mouth.”
Revelation 2:18,26-28 “The Son of God, who has eyes like a flame of fire, and His feet are like burnished bronze, says this... "He who overcomes, and he who keeps My deeds until the end, to him I will give authority over the nations; and he shall rule them with a rod of iron, as the vessels of the potter are broken to pieces, as I also have received authority from My Father; and I will give him the morning star.
The Apostles also taught that Jesus is the Son of God.
Acts 9:20-22 Now for several days he was with the disciples who were at Damascus, and immediately he [Saul of Tarsus] began to proclaim Jesus in the synagogues, saying, “He is the Son of God.” All those hearing him continued to be amazed, and were saying, “Is this not he who in Jerusalem destroyed those who called on this name, and who had come here for the purpose of bringing them bound before the chief priests?” But Saul kept increasing in strength and confounding the Jews who lived at Damascus by proving that this Jesus is the Christ.
1 John 5:5 Who is the one who overcomes the world, but he who believes that Jesus is the Son of God?
Regarding the OP's comment: I took a look at the site you linked to, which I have visited before. I disagree with their statement, "nowhere in the Bible does it say that God had relations with anyone to produce a literal son, nor has Christianity taught that God produced a son through any physical act whatsoever."
While the scriptures do not describe any act of intercourse, the teaching of which would be considered obscene, the Scriptures do indeed teach that God did act, by which he caused Mary to conceive. She did not only become spiritually pregnant, but physically pregnant with the Son of God, as God told her that she would. Mary was obedient and consented, and so she has been blessed among all women.
Luke 1:31-38 And behold, you will conceive in your womb and bear a son, and you shall name Him Jesus. He will be great and will be called the Son of the Most High; and the Lord God will give Him the throne of His father David; and He will reign over the house of Jacob forever, and His kingdom will have no end.” Mary said to the angel, “How can this be, since I am a virgin?” The angel answered and said to her, “The Holy Spirit will come upon you, and the power of the Most High will overshadow you; and for that reason the holy Child shall be called the Son of God. And behold, even your relative Elizabeth has also conceived a son in her old age; and she who was called barren is now in her sixth month. For nothing will be impossible with God.” And Mary said, “Behold, the bondslave of the Lord; may it be done to me according to your word.” And the angel departed from her.
Jesus did not teach that he was only the Son of God in a spiritual sense, and the Apostles taught us that he was the Son of God without any qualification. That is what we first heard and believed.