Because the Nubian Pharaohs portrayed themselves as "Black" and Nubians were portrayed historically as very Sub-Saharan African, and modern Nubians are still very dark. Here is what the Egyptians portrayed Nubians as in the famous set of "foreigners tiles"(the first two): http://realhistoryww.com/world_history/ancient/Misc/Common/Egypt/tile_group.jpg

The actual skin color of Ancient Egyptians is still in debate, as they portrayed themselves with various skin tones throughout their history, and actual mummies are too desiccated to give any good information. They are however -not- entirely either Semites from the Levant, or Sub Saharan Africans.