Here is the quote to which you are referring:
A few graves in the cemetery were marked with crumbling tombstones; newer ones were outlined with brightly colored glass and broken Coca-Cola bottles.
Lightning rods guarding some graves denoted dead who rested uneasily; stumps of burned-out candles stood at the heads of infant graves. It was a happy cemetery.
In this chapter, Calpurnia takes Scout and Jem to her church, The First Purchase Church (a Black church). The children notice right away how different it is from their own church. There is a cemetary out back. Some of the graves in the cemetary are marked with lightning rods. A lightning rod is a metal pole that is supposed to deflect lightning or ground it, so that it will not destroy a structure.
The irony here is that the graves marked by lightning rods must contain people who are not resting easily because why would a dead person have to worry about getting struck by lightning? There really is no logical reason for a grave to have a lightning rod - what is being protected? The corpse? The author is implying that some of the graves probably contain people who died while not at peace, or who died violently, or who died without salvation (since this is a church cemetary).