Q: What did Jesus mean when He said, “It had been good for that man if he had not been born”?

A: First, it is necessary to view the whole verse in a literal rendering.  Quoting from Rotherham New Testament:

“The Son of Man, indeed, withdraws as it is written concerning Him; But alas! For that man through whom the Son of Man is delivered up: well would it have been for him, if that man had never been born.”

While there may be more interpretations, this is my understanding: In this literal rendering when Jesus says “...well would it have been for him, if that man had never been born,”  the “him” is referring to himself, the Son of Man; and “that man” refers to Judas, “that man” who delivered Him up.

In this chapter Jesus told of His being betrayed to be crucified.  Here, I see this as the human side of Jesus, in the view of His sufferings to come.  This has nothing to do with Judas’ punishment.