This is an interesting question, and it is impossible to give you a simple "yes" or "no" due to both national and temporal varieties that existed during the long period of colonialism in Africa, as well as complciations in defining what it meant to be treated "better." Generally speaking, Africans were categorized, and treated, in terms of how close to being "white" they were. That being said, "whiteness" is a fundamental subjective classification and it depended on both the period and region in which colonialism took place. Moreover, it is nearly impossible to do a perfect case-by-case comparison between North Africans, or "Maghribis," and Sub-Saharan Africans. Generally, my answer leans towards telling you that people north of the Sahara were treated better than those south of the Sahara, with some reservations.
My first reservation entails the diversity of people living north of the Sahara. Although most people between say, Cyrenaica, in eastern Libya, and the Atlantic have a broadly similar genetic make-up, their identity does not, and has not, always reflect this identity. Under French rule, for instance, colonial administrators frequently made a distinction between Arabic speakers and "Berber" speakers (consisting of a number of different languages including Riffi, Kabyle, Shilha, and Shawiya). In the French colonial imagination, Berber speakers were tribal peoples who lived primarily in the mountains and had a long rebellious streak. Arabs, in contrast, were plains dwellers who often lived in urban areas who submitted to the rule of some sort of centralized authority--whether in Fes, Algiers, Tunis, etc. French colonial administrators broadly preferred to work with Berberophones due to their perceived rebellious streak against whichever central authority existed in any given region. By working with Berber speakers, the French were able to weaken the authority of whichever central--and typically Arab speaking--authority existed. In return, Berber speakers were given wide-ranging privileges. Although, in reality, Arab speakers and Berber speakers lived side-by-side and in many ways can be classified together as a united body in countries like Morocco, Algeria, and Tunisia. Perhaps the most important divorce between Arab and Berber life took place in 1930, when the French--under the guise of the Moroccan Sultan--issued what is now called the "Berber Dahir." The Berber Dahir gave Berber speakers a status where they were no longer under the central authority of the Moroccan state, and instead followed Berber customary law.
In Algeria, the French favored Berber-speaking Kabyles over Arab Algerians and many of the so-called "Harkis" of the Algerian War were Kabyles. Later, they were granted greater access (although by no means easy access) to French nationality and, eventually, citizenship. Because of these greater rights under the colonial administration, Kabyles often held a higher sense of loyalty to French colonial rule than Arab speakers in neighboring regions. For many Arabs living in both Morocco and Algeria, conditions of colonial rule were quite similar to that of other parts of Africa.
My other example comes from the region south of the Sahara: Rwanda. Rwanda is a fascinating country made up of two large ethnic groups, the Hutus and the Tutsis, and a significantly smaller one, the Pygmies. Before the First World War, Rwanda was colonized by Germany, alongside Burundi and Tanganyika (then, German East Africa). Before the onset of German colonialism in the region, these three ethnic groups did not exist. Although there were some distinctions, they were not discrete groups. When Germans arrived, they latched closely onto the Tutsis, arguing that they were much better than Hutus and would be able to function within the colonial administration. The Tutsi people in Rwanda were frequently shepherds who took care of livestock, in contrast to Hutus who more generally grew crops. In addition, Tutsis were seen as being taller and having lighter skin than Hutus. Upon establishing these descriptions, German racial theorists argued that Tutsis must have been "Caucasoid," coming from northeastern Africa, around Ethiopia and Somalia, in contrast to Bantu, or in the conceptualization of the Germans "Negroid" Hutus. As a result, Germans gave Tutsis more meaningful positions with higher pay and many were placed in the colonial bureaucracy. With the German defeat in World War I, both Rwanda and Burundi passed into Belgian hands, and they maintained the ethnic distinctions produced by Germans. Over the course of the coming decades, the German construction of "Hutus" and "Tutsis," as well as their elevation of the Tutsis, gave strength to rising ethnic tension and eventually widespread Tutsi control with Rwandan independence. Resentment of Tutsi control continued to rise, and eventually culminated in the Rwandan Genocide of the 1990s.
Although neither of these case studies directly answer your question, I think they tell us a lot about the production of race and ethnicity, including the way that Europeans thought about "whiteness." It is clear that there was a hierarchy of whiteness in European minds as colonial rule became rooted throughout the African continent, and this "whiteness" hierarchy impacted administration and rule in tangible ways, continuing to the present. I maintain that there is no easy answer to this question, but broadly speaking, yes, North Africans were treated 'better' (although colonialism never treated any colonized subject in a 'good' way, by any classification) than those south of the Sahara, with exceptions of moments of extreme imperial crises like the Algerian War and the so-called "pacification" of Libya, which both saw the rise of concentration camps and mass executions, much like in South Africa during the Boer War, Namibia during the Herero Genocide, and Kenya during the Mau Mau uprising.
Sources
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Brown, Kenneth. “The Impact of the Dahir Berbère in Salé.” In Arabs and Berbers: From Tribe to Nation in North Africa, edited by Ernest Gellner and Charles A. Micaud, 201–15. Lexington, MA: Lexington Books, 1972.
Crapanzano, Vincent. The Harkis: The Wound That Never Heals. Chicago: University of Chicago Press, 2011.
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