Yet even this great man, this great prophet, John the Baptist, doubted. In the depth of the dark dungeon John began to doubt. Jesus was not working in the way John thought He should.
The dark places we enter in life are dreadful places which can become the breeding ground of doubt.
John the Baptist, who was in prison, heard about all the things the Messiah was doing. So he sent his disciples to ask Jesus, "Are you the Messiah we've been expecting, or should we keep looking for someone else?" Jesus told them, "Go back to John and tell him what you have heard and seen—the blind see, the lame walk, the lepers are cured, the deaf hear, the dead are raised to life, and the Good News is being preached to the poor. And tell him, 'God blesses those who do not turn away because of me'" (Matthew 11:2-6).
In the darkness of his dungeon, John the Baptist began to wonder if Jesus truly was the Messiah.
John thought Jesus was coming in judgment because he did not understand the two different stages of the Messiah's coming. Jesus came in mercy at His first coming and He will come in judgment at His second coming.
Many doubts originate from thinking God is not working the way we think He should. We don't see the whole picture right now.
Don't stumble in doubt when God works in a different way than you are expecting. (Commentary Mark Martin)