Cleopatra was of Greek origin, she was not black. It's true that some of the Pharoahs were black, but not all of them were even African (for example the Persian dynasty).
Genetically most were mixed race due to diplomatic marriages between kingdoms in the ancient near east (from Africa to Southern Europe); and depictions show that basically they looked like Egyptians do now i.e. varying in colour and look from very dark to very pale, varying in face type as well.
So, no problem with Jolie being cast as Cleopatra BUT I wish they would make movies about other Egyptian Queens who to be honest have more interesting back-stories e.g. Hatchepsut, who ruled the country about a thousand years before Cleopatra; Nefertiti and her daughter Akhensenamun who were around during a period that makes Rome look like the average episode of Play School. Then you have the wives of Ramesses III who tried to bump him off...