What factors contributed to the development of segregation in the late nineteenth century?

The big one I can think of is the emergence of the political power of blacks (which contributed strongly to racism), and with this the Populism movement, that eventually collapsed into a group of uber-racist radicals. Also, social philosophers like Booker T. Washington and W.E.B. Dubois and their different views/efforts. The social divisions, as well as cultural divisions with the creation of Jazz and a unique African-American fusion culture. Jim crow laws, but I guess you already mentioned that with black codes. The continuing struggle between the republicans who advocated equal rights and the democrats who supported strong racism sort of built a shaky and fragile compromise with the "Separate but Equal" idea that came from Plessy v. Fergusson. On a side note, with the rapid growth of cities and mass transit systems, people (not just blacks) were separated from one another based on social status, heritage, race, beliefs, etc. Jews grouped together, as did Italians in Little Italy, Chinese in Chinatown, and all the other many subidivisions, so it seemed only appropriate that this happen to Blacks as well, but to a slightly greater degree.