Controlling all of Africa, from the Mediterranean to the Cape is not exactly as easy as it looks. One of the most obvious challenges would be taking over the interior, and while the stronger coastal states are present no European state of the Early Modern era would be able to muster the forces needed. The Ottomans, with an early standing army would be in a better position, but they had limited supply lines and would be fighting a mostly overland campaign.
Not to mention that Africans could defeat colonial armies from Industrial states in the 19th Century, the Tuareg and the Zulu are two examples I can name offhand, along with Ethiopia gaining the distinction of doing that and keeping their would-be evil overlords out. If we're talking an Early Modern European state, much of the interior is uninhabitable due both to hostile natives and to disease. If religious motivations underline it, the Muslims and Indigenous religions would both have reason to start kicking ass. If profit....either Europe or the Ottoman Empire would have to be *really* low on salt to start embarking on crusades into the interior Sahara. The jungle country even today can't support a number of people, and this with much greater transportation and things like air conditioning. And with the technological bases available to Early Modern societies, nothing of the resources there are discoverable or financially viable for Christians or Muslims.
And conquerors don't tend to conquer just for the Hell of it.