There are two major reasons for this.
First, children are deemed to be less culpable for their actions than adults are. Part of the logic of treating children differently is the idea that they are not as responsible for what they do. They do not yet have the mental capacity to understand the morality of what they are doing or the likely impacts of their actions on themselves or others.
Second, children are seen as less fully-formed and more malleable. Because our society believes this, it believes that it is more possible to rehabilitate children than to rehabilitate adults. This affects the nature of the punishments handed out in the juvenile justice system.
In these ways, children are treated differently because they are not seen as fully developed human beings. They are seen as less culpable for the actions and it is believed that they can change more readily under rehabilitation than adults can.