Hughes is not criticizing Christianity in this story. He's showing how the adults in a child's life can confuse him/her if they don't fully explain things to the child.
Langston loses his faith because of Auntie Reed. She tells him that "when you were saved you saw a light, and something happened to your insides!" Langston took this literally, expecting to actually see a light and to feel something happening in his body. When he doesn't see or feel anything after he's saved, Langston gives up on believing in Jesus because he believed his aunt's descriptions of salvation. His confusion worsens when Westley gets saved because he knows Westley didn't experience anything such as a light and is lying. Langston goes up to be saved only because he doesn't want to disappoint the adults, and they are all telling him to come up and be saved.
That night, Langston cries because he lied, showing he is a good Christian because he believes the commandment about lying. His aunt misreads his tears and tells her husband he's crying because he's experienced the Holy Ghost and seen Jesus.
The story reflects how adults don't realize or understand how children think, especially when it concerns a concept as difficult as faith. Auntie Reed expects Langston to accept what she says because she's the adult, and he's a child. She never explains that Biblical stories are a useful guide for how to live one's life.
Hughes isn't criticizing any faith in this chapter in The Big Sea, one of his autobiographies. Instead, the story shows how the adults confuse the children when they don't explain their religious metaphors. Langston's loss of faith is caused by Auntie Reed. She tells him that "when you were saved you saw a light, and something happened to your insides!" Langston takes this literally, expecting to see a light and to feel something happen to him. When Langston doesn't see or feel anything, he gives up on believing in Jesus. Langston lies and goes up to be saved only because he's the only child left. That night Langston cries because he lied, showing he's a good Christian because he's aware of the commandment against lying. Auntie Reed misreads Langston's tears and tells her husband that Langston is crying because he has experienced the Holy Ghost and saw Jesus. The adults in Langston's life don't realize or understand how a child thinks and expects him to accept something just because they have told him it's the right thing to do. They don't explain that Biblical stories serve a useful guide for living one's life.