Earlier, Silas said the Freedom of the Graveyard protects Bod. It’s likely because of this that Bod isn’t afraid of the Indigo Man—as far as Bod knows,
nothing in the graveyard can hurt him. And especially since the Indigo Man doesn’t behave like a normal ghost, it’s a clue that something is amiss here. Bod shows that he’s a rational, logical child who doesn’t let fear get the better of him. Because he has this skill, he’s able to talk Scarlett through this scary situation.