The pillbox in Chapter 39 of Maniac Magee bothers Maniac so much because it is a symbol of racism. He finds out that the Cobras are building the pillbox because they think that they will need to fight the black people from the East End. Because Maniac knows many of the black people, the Cobras’ racism bothers him deeply.
Remember that by this time in the book, Maniac has spent a lot of time living in the East End with the African Americans who live there. While he was driven out of the East End, there are many African Americans who were his friends and he knows to see blacks as individuals. By contrast, the Cobras do not see the African Americans as regular people. They see them as a threat to be defended against. They believe that the African Americans are “today’s Indians” and are “bloodthirsty for whites.” Maniac cannot take being around people who feel like this. He hates racism because he has gotten to know the African Americans in the East End. Therefore, “there was no room (in the McNabs’ house) that Maniac could stand in the middle of and feel clean.” The racism that was demonstrated by the building of the pillbox disgusted and bothered him.