The Misfit is explaining his history to the grandmother when he says this line. Just prior, she said "Jesus, Jesus" again and again, implying that Jesus could help him, "but the way she was saying it, it sounded as if she might be cursing." The Misfit picks up this thread because he agrees that Jesus deserves to be cursed. He says, "'Jesus thown everything off balance. It was the same case with Him as with me [...].'" Essentially, when Jesus took humankind's sins on himself -- sins he did not actually commit -- he threw off the balance between guilt and punishment. Jesus was not guilty of anything and yet he endured a terrible, painful punishment. In doing so, the Misfit thinks that he set the precedent for punishing people who haven't actually done anything wrong.
The Misfit was innocent, too, and yet he was punished terribly. He says,
"I never was a bad boy that I remember of [...] but somewheres along the line I done something wrong and got sent to the penitentiary [....]. I set there and set there, trying to remember what it was I done and I ain't recalled it to this day."
He was told that he was in prison because he killed his father, but his father actually died of pneumonia, and the Misfit had nothing to do with it. He had committed no sin, no crime, and he had to endure a punishment, too, and so he blames Jesus for being the one who seems to have told society that this was an acceptable thing to do: to find a scapegoat for their problems and blame and punish him. This is why he calls himself the "Misfit"; "because [he] can't make what all [he] done wrong fit with all [he] gone through in punishment."