First, Jesus tells the disciples "one of you will betray Me". Now I realize that all of the disciples in some sense betrayed Jesus. But Jesus tells Peter that Peter would deny Him. In fact, Jesus explains that the Shepherd would be struck and the sheep would be scattered by quoting Zecharia 13:7. This was after Judas had left and was separate from the rest of the disciples. In this case, Peter most certainly represents the rest of the disciples.
So let me make this clear. Jesus never says that the disciples would betray Him. Only one receives that label. He also makes clear that He prayed for Peter and the rest of the disciples to be restored. Once again, we must ask if Jesus' prayer must also be applied to the Betrayer Judas? The answer should be obvious.
Now to the issue of the phrase, "son of perdition" or "destruction".
John 17:12 While I was with them, I kept them in your name, which you have given me. I have guarded them, and not one of them has been lost except the son of destruction, that the Scripture might be fulfilled.
We must see again that Jesus never calls the other disciples "son of Destruction". He only refers to Judas with that title. But what does he mean by it? Well, let's take a look. After Jesus explains that Judas would betray him Him he makes a very troubling statement.
Mat 26:24 The Son of Man goes as it is written of him, but woe to that man by whom the Son of Man is betrayed! It would have been better for that man if he had not been born."
Yes, it would have been better for Judas to not have been born! The horror of such a thought is incredible. Jesus gives us information about the destiny of Judas. In a note about Matthew 1:1 and 11:19, commentator Barnes offers this insight about the phrases when "son of..." is used.
The term son was given by the Hebrews to those who possessed the character described by the word or name following. Thus, sons of Belial - those who possessed his character; children of wisdom those who were wise, Mat_11:19. Thus Judas is called a son of perdition because he had the character of a destroyer. He was a traitor and a murderer. And this shows that he who knew the heart regarded his character as that of a wicked man one whose appropriate name was that of a son of perdition.
Again, please note Jesus is making a clear break and distinction between Judas and the rest of the disciples. Jesus is making and adopting the disciples to be "sons of God" [John 1:12] through His saving work except Judas.
This idea is similar throughout all of Scripture. See Genesis 3 and the promised Seed.
Gen 3:15 I will put enmity between you and the woman, and between your offspring and her offspring; he shall bruise your head, and you shall bruise his heel."
Perhaps it truly bothers us that one could be so close to Jesus and yet be ordained a "son of destruction". Perhaps it bothers us that Jesus did not pray for Judas as He did the other disciples. Perhaps it bothers us that God has such freedom to save whom He will, and we do not. Perhaps we are bothered by a Scripture and Word of God that confronts our traditions that we so strongly desire to cling to. Perhaps it is all of these things and more.
My brothers and sisters in Christ, I pray that we would think logically and clearly about such issues. But even more importantly, I pray that we would listen to God's Word with repentant hearts. For in fighting the truths of Scripture, are we not all doing the very things the Disciples did that last night? We all think we would never deny our Lord. But what about His Word?