The name Darfur is from dar fur which in Arabic means "the abode of the Fur". The Fur are the predominant ethnic group in the Darfur region. The Fur began to be converted to Islam in the 1300s or 1400s. In 1596, the Darfur Sultanate was established and Islam declared the state religion. The Darfur sultanate remained independent through various conflicts in Sudan including the Anglo-Egyptian conquest of Sudan in the late 1800s before finally being subjugated by the British in 1916 and made part of Sudan. You can read a brief history of the Darfur Sultanate.
Fouad Ibrahim of the University of Bayreuth in Germany provides a brief outline (PDF) of his ideas on the Darfur conflict. He gives emphasis to Darfur's long history of independence and its resistance to various other groups seeking control of all of Sudan.
I also found a paper by Mohamed Suliman of the Institute for African Alternatives written in 1997, which looks at the roots of two conflicts in Western Sudan, one of which is Darfur. He argues that although the indigenous peoples of Darfur (the Fur and several other tribes) and the Arabs have always had distinct identities, they generally got along well until resources became scarce, then they made ethnicity and race the focus of their conflict:
As to Darfur prior to the mid-1980s, conflicts in northern Darfur were infrequent, highly localised and of low intensity. Arab pastoralists were allowed into Jebel Marra after the harvest was collected and usually stayed there until the first rains in April or May. Indeed, some of their livestock belonged to rich Fur peasants. Ethnic barriers were low and easily surmountable. All people inhabiting the area were Sunni Muslims with Arabic as their lingua franca. The prolonged drought dealt a severe blow to the tradition and spirit of cooperation and tolerance between herders and peasants in the region. Fuelled by the neighbouring conflict between Chad and Libya and the influx of modern weapons, skirmishes turned into large-scale armed conflict. On both sides of the conflict divide, people fell back to their time honoured, traditional group solidarity and reciprocity. The barrier between the Fur and their erstwhile good neighbours began to grow. People found solace in entrenchment within their ethnic and cultural niche. The conflict was widely perceived as ethnic/tribal. Party political affiliations, which ran across ethnic and geographical borders, began to collapse. Ethnic brotherhood became paramount and the conflict was seen by all as an ethnic strife. Fourteen years later, the transformation of the perception of the conflict into an unshaken conviction about the true nature of the conflict is proceeding fast. The ethnic divide already constitutes, for good or for evil, a formidable social force in northern Darfur. Without a comprehensive solution to the protracted conflict, that also restores the economic and social fabric of the region, renews cooperation between the two factions and opens new vistas for economic and social development, the spreading malaise of ethnic hostility will continue to grow. In its wake, efforts at conflict resolution will be hampered and the palpable presence of ethnic hostility will indeed constitute a concrete and tangible cause of future violent confrontations. Most violent conflicts are over material resources, actual or perceived. With the passage of time, however, ethnic, cultural and religious affiliations seem to undergo transformation from abstract ideological categories into concrete social forces. In a wider sense, they themselves become contestable material social resources and hence possible objects of group strife and violent conflict. Usually by-products of fresh conflicts, ethnic, cultural and spiritual dichotomies, can invert with the progress of a conflict to become intrinsic causes of that conflict and in the process increase its complexity and reduce the possibility of managing and ultimately resolving and transforming it.