In terms of ethnic cleansing, there's a lot of cases in history where religion has been the main culprit. In the Roman Empire, there was persecution of Christians, in order to protect the Roman God system. Across many European countries in early history, Jews and Muslims were banished and killed in many countries. More recently, the Jewish massacre in the holocaust was an action of the Christian Hitler and now, Islam Jihadists in the middle east are engaging in ethnic cleansing. It seems a common trend for religious based groups in society to ethnically cleanse. Now, there is a lot of non-religious cases but the majority of ethnic cleansing cases through history seem to be over religion.
By Croations for political and cultural reasons. Religion had little, if anything, to do with the "origin" of ethnic cleansing.
Note: by definition there is a difference between genocide and ethnic cleansing. Genocide has the purpose of complete or partial destruction of a target group. Ethnic Cleansing is forced deportation. Although ethnic cleansing can turn into genocide.