What does the narrator mean when he says that everyone at the funeral is in the box with tod clifton?

The narrator is implying the way that Clifton's demise and its motivation were conceived of bigotry. This symbolizes the way that what happened to Clifton could happen to any of them. The way that Tod Clifton could be gunned down for punching an officer, without any repercussions against the officer, implies that the world outside Harlem is not a sheltered place for blacks. Everybody is jeopardized in an atmosphere where such things are allowed.