Dubois was reacting to Booker T. Washington's famous speech (1895) in which Washington proferred a "compromise" to a county torn by the political situation of the post-emancipatory era. In an effort to appease both liberals and conversatives, Washington said, "In all things purely social we can be as separate as the five fingers, and yet one as the hand in all things essential to mutual progress."
The meaning was that black folk could have their own culture and whites another, but when it came time for political and social agendas, the country must come together as a single entity.
Dubois intially applauded Washington's compromise, but later changed his mind. The "seperate but equal" ideology may have seemed good in theory, but in reality it served to further reinforce divisions. Dubois argued that though well-meaning, the reality was that racists were using the division to keep blacks out of higher education and better paying jobs.