What does John 16:3 mean?

Jesus is warning His followers that persecution will come (John 16:1), and it may become brutally violent (John 16:2). The reason for giving these dire predictions is to strengthen faith. Believers should recognize that hardship is not something which catches God by surprise. Rather, this is exactly how He told us things would play out. In the previous verse, Christ pointed out that some of the most brutal oppression will come from those who think murdering Christians is an act of good!

Clearly, as stated here, those who assault believers do so because they, themselves, have no relationship with God. Earlier, Jesus pointed out that love for one another was a primary sign of faith (John 13:34–35). Here, we see the other side of that: hateful persecution of believers is a clear sign of someone—or a culture—disconnected from saving faith. Those who hate and harm believers do so because they are deeply, spiritually opposed to God and to His Son (1 Peter 2:3–4; John 15:18).