Homophily might seem benign, but what may start out as preference can easily become segregation. Famous economist, Thomas Schelling's work in "Models of Segregation" (1969) showed the impact of preference.
"In this paper he showed that a small preference for one's neighbors to be of the same color could lead to total segregation. He used coins on graph paper to demonstrate his theory by placing pennies and nickels in different patterns on the "board" and then moving them one by one if they were in an "unhappy" situation. The positive feedback cycle of segregation's causing increased prejudice, and prejudice's increasing preference for separated living, can be found in most human populations. Variations are found in what are regarded as meaningful differences – gender, age, race, ethnicity, language, sexual preference, religion, etc. Once a cycle of separation-prejudice-discrimination-separation has begun, it has a self-sustaining momentum.
He further postulates in his 1978 book Micromotives and Macrobehaviors that a preference for segregation of two groups and a preference to congregate with others of your demographic are indistinguishable as motives which could explain the phenomenon of voluntary separation of two distinct groups."