It is a source of community, education, employment, moral instruction, and political mobilization, in short, "all that great world from which the Negro is cut off by color-prejudice and social condition." He traces its origins to slave society, noting that nascent religious communities developed within slave populations, fulfilling many of the needs of black people. So in many ways, the modern (i.e. turn of the century) black church fulfills a role similar to that under slavery. He also analyzes the development of black theology, noting its loose associations with white evangelical denominations. Unlike later historians that would emphasize religion as a site of slave agency, Du Bois claims that African religion was more geared toward submission, or "an infinite capacity for dumb suffering" because of its emphasis on the afterlife. Religion became a force for liberation not on the plantations, but among the free black communities of the North, where it strongly informed abolitionism.

Du Bois detects the same split among contemporary blacks, some of whom tend toward radicalism, the other (like Booker T. Washington and other reformers based in the South) toward "hypocritical compromise." In the North, however, many who are not grounded in the church or other institutions turn to crime. In other words, in keeping with the argument of the whole book. Du Bois sees the church as instrumental in effecting black reform, but notes that its effects have been complex and often contradictory, largely due to exclusion from the opportunities available to white society.

The main idea animating The Souls of Black Folk is that Black people must fight back against racism and injustice if they are going to save themselves. It is a resounding and heartfelt attack on the dominant ideology of race relations in the late nineteenth and very early twentieth century.

Booker T. Washington's ideas of Black accommodation to white supremacy were dominant when Du Bois wrote his book. In an 1895 speech called the Atlanta Compromise, Washington argued that Black people should temporarily abandon ideas of equality, including the right to vote, equal access to education, and an end to segregation. Instead, he said they should accept second-class citizenship, pursue vocational work, such as being railroad porters and shoeshine boys, and build up an economic base. By becoming financially solid, Washington reasoned, Black people would win the respect of white people and then could claim full equality.

Du Bois, a Harvard-educated Black man with a PhD who had studied at prestigious German universities, was highly alarmed at Washington's ideas. He feared that following Washington's formula would cause Black people to internalize inferiority and lose their souls. He uses the example of present-day Greeks to make his case, saying that this once proud and intelligent people has been ground down to internalized self-hatred and inferiority by centuries of oppression.

Du Bois uses his book to famously discuss the sense of a double identity that Black people have, in which they are forced to see themselves in the diminished way white people see them as well as the more humane way they see themselves. He argues forcefully that to achieve success, Black people must not compromise, but must struggle for full equality. He set out a full civil rights agenda very similar to that of Martin Luther King in the 1950s and 1960s.