From what I can remember, states' rights was a large factor contributing to the Civil War. With Lincoln becoming president and representing the North, the Southern states seceded, leading to a war. The state governments of the South argued that since the Constitution and the federal government was created by the states, the federal government had no right to stop states from seceding. President Lincoln and other northerners disagreed and wanted to preserve the Union by stopping states from seceding.
After the war, I believe the South still disagreed on a strong federal government. They wanted to rule the area by themselves.
The Atlantic Charter can be seen as a statement of intention and vision: the intentions of the leaders of the UK and the US about the world after the World War.
Specifically, they believed in the self-determination of the countries, which means that the countries would have the right to govern themselves.
They indented this Charter to apply to Europe only,for example Poland, but later the African countries used it as an argument for de-colonisation.