We live in a society that is more and more segregated along racial and economic lines, with poor people of color living and working in different areas than middle-class whites. The result is a society which excludes people of color from full participation in the economy and the community.
One result of this is that our prisons are filled with people of color. To then further segregate these prisons reinforces negative racial stereotypes and destroys any feeling of self-worth, which is the basic element for rehabilitation and re-entry into productive society.
Worse still, racial segregation and racial conflicts are often manipulated by institutional administrators to further institutional control at the expense of prisoners' rights. This is particularly true of the manipulation of gang violence in the state prison system. Separate but equal can never be equal.