Jesus had known from the beginning which of them did not believe and who would betray him. (NIV)
1. Some Trinitarians act as if this verse proves that Jesus was God just because the word “beginning” is in the verse. Nothing could be further from the truth. Even a cursory word study will show that the word “beginning” has to be defined by its context. Any good lexicon will show that the word “beginning” is often used to describe times other than the start of creation. Examples abound: God made them male and female at the “beginning,” not of creation, but of the human race (Matt. 19:4). There were “eyewitnesses” at the “beginning,” not of creation, but of the life and ministry of Christ (Luke 1:2 and 3). The disciples were with Christ from the “beginning,” not of creation, but of his public ministry (John 15:27). The gift of holy spirit came on Peter and the apostles “at the beginning,” not of creation, but of the Church Administration that started on the Day of Pentecost in Acts 2 (Acts 11:15). John 6:64 is simply saying that Christ knew from the time he began to choose the Apostles which one would betray him.
2. When this verse is understood in its context, it is a powerful testimony of how closely Jesus walked with his Father. First, there is nothing in the context that would in any way indicate that the word “beginning” refers to the beginning of time. Jesus had just fed the five thousand, and they said, “Surely this is the Prophet who is to come into the world” (6:14). Right away that tells you that the people did not think Jesus was God, but a prophet. The people wanted to make Jesus king, but only because he filled their stomachs (6:15 and 26). When he challenged them to believe in him (6:29), they grumbled (6:41). As Jesus continued to teach, the Jews began to argue among themselves (6:52), and even some of Jesus’ disciples began to grumble at the commitment Jesus was asking from them (6:60 and 61). Jesus, knowing his disciples were upset with his teaching, did not back off, but rather pressed on, even saying that he knew some would not believe (6:64). The result of this discussion was that some of his disciples left him (6:66). Since some disciples left him after this teaching, it would be easy to say that perhaps Jesus acted unwisely by pressing on with his difficult teaching. Not so. Scripture reminds us that Christ knew from the beginning who would not believe, and even who would betray him. Thus, he also knew that his hard words would not drive any of the true sheep away. The “beginning” being referred to here is the beginning of his ministry. When he started gathering disciples and apostles and teaching them, God showed him by revelation who would believe and who would betray him.
Snedeker, p. 215