There are a couple of tough challenges in this passage. Firstly, the prophecy from Isaiah quoted in verse 40 by John is not just a challenge for this passage, but is quoted or echoed in Matthew 13 v 14-15, Mark 4 v 12, Luke 8 v 10, Romans 11 v 8, 2 Corinthians 3 v 14, Acts 28 v 27: so,throughout the New Testament. It appears to say that peoples' unbelief is due to God's action, therefore God has ordained that certain people must not and will not ever be able to believe. And yet John 3 v 16 states clearly that Jesus came to be the Saviour of the whole world!
Let's think back to Isaiah's situation: he had prophesied using the words God had given him and still people refused to listen and change their ways. He had put everything into it and his words spring from a broken heart. For the Jews, God was behind everything, nothing could happen outside His purposes. When we read these passages then, we can understand them as saying that even unbelief can be used to further God's eternal purposes. These Jewish listeners in this passage did not believe in Jesus, that was their free will choice, it was not God's fault: but, even that somehow has its place in God's plans. As Paul saw it, the unbelief of the Jews was used by God for the conversion of the Gentiles-Romans 11 v 11,12.
The second challenge is that Jesus came into the world to bring light, hope, salvation, God's Kingdom. It was not the wrath of God which sent Jesus to the world, but His love (John 3 v 17). Yet, the coming of Jesus inevitably involves judgement and this is what we've seen as we've studied the preceding chapters. No body could sit on the fence. By our reaction to Jesus we show what we are-we therefore judge ourselves. If we worry too much about what others think, or if we have something to hide, or feel we have too much to lose, then we prevaricate or turn away from Jesus.
I did some door to door visits when we lived in Wrington and one house I visited was of a couple in their sixties. They were happy to see me, but when I talked to them about Jesus and about coming to church, they excused themselves as being too busy, maybe one day they would have time. Both died within a year. The call of the Gospel is for today- Hebrews 3 v 15.