Yes, it means that you put the bread in the bread box. It's present simple and it's describing a habitual action or state. It's like saying the bread 'lives' in the bread box. The milk goes in the fridge. The shirts go in the wardrobe.

In this sentence, "the bread goes in" is using the present simple tense, but it's not a command. It describes a general fact or routine action—how things usually happen. So, "the bread goes in the bread box" means that, as a standard procedure, the bread is placed in the bread box. It's more like an explanation of where the bread is supposed to go rather than giving an immediate order (like "Put the bread in the bread box"). It’s similar to saying, “The bread belongs in the bread box,” or, “It’s normally placed there.”