"Tom Robinson is a mild-mannered, conscientious black man whose kind acts earn him only trouble when Mayella Ewell accuses him of rape." He is an "innocent" because he trusted Mayella, he even says he "felt sorry for her." Tom never dreamed that helping this young white girl could get him into so much trouble. Tom also demonstrates innocence when he trusts the judicial system to do what was right. Tom never hurt anyone and looked at the world through the eyes of a trusting caring man.
He got his arm stuck in a cotton press and his arm is crippled so he couldn't have beaten her.
Tom is innocent because he is also innocent of mind. Tom is crippled so there is no way that Tom could have beat Mayella, but while Mayella was rude to Tom, Tom felt compassion for her and still tried to be nice even though she was the cause of his death.