The students at Trinity, a Catholic high school for boys, are supposed to be getting a religious education. Instead, they're mostly being taught how physical and psychological violence can be used to manipulate others. Too bad it's not a school for super villains, because it'd the best in the world. The hero of The Chocolate War, Jerry Renault, makes a symbolic stand against the bad educational practices at Trinity by saying "No" to selling chocolates for the school. He suffers a lot for doing this, and the lesson he learns at the end of the book may not be the warm, fuzzy thing you might expect.
The "real world" is a ruthless place; Trinity is simply preparing its students for this world.
Jerry models non-violent resistance for his peers.