What do you doubt in your understanding of the Scriptures? When have you most doubted? How do you feel about these doubts? What do you typically do with them?

I know for myself, doubting was often regarded as some sort of sin, like a first cousin of 'blaspheming the Holy Spirit'. As I engaged in Seminary, doubt was then seen as an obstacle to overcome with cognitive exercises and sheer intelligence. As a husband and dad, doubt is often laced with guilt and is tinged with despair. As a grown man acquainted with brokenness, sorrow and grief, doubt is an ever-present part of my life.

Read this section from John 20 and pay attention to your impression of Jesus.

"Now Thomas, one of the twelve, called the Twin, was not with them when Jesus came. So the other disciples told him, “We have seen the Lord.” But he said to them, “Unless I see in his hands the mark of the nails, and place my finger into the mark of the nails, and place my hand into his side, I will never believe.”
Eight days later, his disciples were inside again, and Thomas was with them. Although the doors were locked, Jesus came and stood among them and said, “Peace be with you.”  Then he said to Thomas, “Put your finger here, and see my hands; and put out your hand, and place it in my side. Do not disbelieve, but believe.”  Thomas answered him, “My Lord and my God!”  Jesus said to him, “Have you believed because you have seen me? Blessed are those who have not seen and yet have believed.”

What tone do you hear in Jesus' voice?
Now imagine his facial expression and his body language, what message do they convey?

Realize that most of how you read his voice and expressions comes from your own experiences; the teacher who scowled at you when you didn't know the answer, the parent who lectured you when you mistrusted their direction, the preacher who yelled about the doubting Thomas, and so on.
Read the passage again if need be, but pay attention to the response of Jesus to Thomas. His doubt was never held in contempt, if it were, Jesus would never have shown up. Rather, Jesus had compassion on his old friend. Consider this, Jesus had appeared to many of his friends the day of his resurrection, but not to Thomas. Jesus knew his doubts and a week later sought him out and implored him to believe, offering up his open wounds as evidence. He would not have done so if he considered his doubts something sinful or rebellious. Jesus empathetically engaged the doubts of Thomas.

Then, Jesus takes it a step further when he talks about the blessedness of belief. This 'Blessed are those who have not seen yet believed' is spoken by the same man who preached about blessedness on the Mount of Olives in Matthew 5-7. There was no sarcasm in his voice. He was not throwing shade at Thomas for needing to see his wounds. He was stating that those who believe without seeing, doubts and all, are blessed.

I encourage you to be like the father in Mark 9:24. With little more than doubt and despair he asked Jesus to do something, anything at all to help, and then cried out 'I believe, help my unbelief'. This doubtful confession of faith seems enough, as Jesus went on to heal and restore. The point is, unwavering assurance is not the highest mark of faith, but rather bringing what you have- your confused, doubtful, teetering faith- and trusting it as you can to the compassion of Jesus is our goal.