What does John 5:41 mean?

Jesus has just given three forms of evidence to support His controversial claims (John 5:18). These fulfill the requirements of Jewish courtroom law (Numbers 35:30; Deuteronomy 17:6). At the same time, truth is truth, whether anyone accepts it or not. Jesus is graciously speaking to people according to their natural human weaknesses (John 5:34). Unfortunately, many who heard His words refused to accept Him (John 5:38). This, more than any evidence, was the reason for their rejection: they simply refused to believe, no matter what (John 5:39–40).

Jesus' statement here is being made in that context. Certainly, Jesus accepted worship and praise from men (Matthew 14:33; Luke 24:52; John 9:38). What He means in this conversation is that whether people accept Him does not change the fact that what He says is true. Jesus will point out that He is the only One with certain kinds of knowledge, so it makes sense that He alone could be a witness about them (John 8:14). This is meant to counter part of the Jewish religious leaders' attack on Jesus.

It's possible these critics thought Jesus was angry because they would not approve His message. Instead, the point is that He does not need their approval. He follows the will of the Father, whether these men accept Him or not. Since they had already made up their minds to reject Him (John 5:39–40), their endorsement will never come anyway.