There were a few practical obstacles that made colonising Africa a particularly tricky proposition:

• You couldn't exactly stroll in. European armies had little to no military advantage over the organised and well-armed polities that occupied much of Africa (particularly the north and west) at the time. This was not a matter of sending relatively small expeditions to claim new lands. For example, as late as 1578 Portuguese attempts to interfere in Morocco resulted in a crushing defeat when an army of 20k was wiped out by the Moroccans at the Battle of Alcazar. It wasn't until centuries later that Europeans would possess advantages great enough to make the likes of Omdurman possible. Even then it often took protracted wars to enforce European rule on parts of Africa.

• Go farther south from the Maghreb and you'd encounter an even more difficult opponent: disease. West Africa in particular was not a place that Europeans wanted to hang around in. The local diseases, in particular malaria, were an effective barrier to any inland penetration. This persisted right up to the development of effective anti-malarial treatments. Until the development of quinine (ironically, an import from the New World) West Africa was nicknamed the 'white man's grave'; as late as the early 19th C British garrisons in the area had a death rate of up to 80%.

So there was nothing particularly easy about colonising Africa. Hence the Europeans tended to settle into a pattern of coastal trading stations. They traded with locals (most notoriously for slaves) and therefore avoided having to venture into the hostile and challenging terrain of the interior. With some exceptions (eg S Africa) that attitude didn't really begin to change until the mid-19th C.

Thomas Pakenham's The Scramble for Africa is a good introductory work on European colonisation of the continent. Abernethy's Dynamics of Global Dominance takes a more theoretical approach but also puts forward some good reasons for why imperialism developed as it did. I just wish I could still remember half of them...

I think your view of precolonial Africa might be a little skewed. Africa was a continent of great and powerful empires. Take a look at this topic from the FAQ. These empires could field armies with thousands of troops at a time when the British Isles weren't unified under a single flag, Italy was a collection of city-states, Germany was composed of dozens of warring principalities, Spain was in civil war and France was a collection of warring nobles nominally under a King. If a nation somehow managed to get together an army strong enough to Conquer in Africa say 60,000 troops (The French force at Agincourt and the British Army strength in the American Revolution.) Considered a large army at the time. Those troops would have returned home to find their own country invaded while it's army was away.

Disease killed off a large portion of the population of The Americas perhaps as high as 90%. This left a huge landmass filled with gold silver and cultivatable exotic plants like coffee tobacco chocolate and sugar. With no strong empires to oppose colonization. But there was nobody to work the plantations or mines. So the Europeans looked to Africa where slavery had a long history. Powerful African rulers happily sold some of their slaves in exchange for European goods such as guns, and also for the same products the Europeans were bringing back from the Americas.

over the course of about 200 years from the early 1600's to the early 1800's Europe gradually weakened the power of African Empires by paying them to war against each other for slaves. It was not until the middle of the 19th century when the industrial revolution had made Europe powerful enough militarily and 250 years of slave wars had weakened Africa that Europe was truly able to colonize Africa.

Ask yourself, why would someone from europe want to uproot their entire life to go live in Africa? First you have to contend with the vast numbers of people that already live there many of whom are under the control of powerful states whether they be muslim lands or not. Then what are you getting out of it? What economic advantage is there to living in Africa over europe where you speak the language and know how to work the land. Lastly why are you going to go live in this completely foreign land where you will most likely die of diseases that you have never encountered before in a climate you are not familiar with. You don't even really have a technological advantage at this point.

A much better question would be what drove Europeans to colonize Africa in later centuries. The stakes, motivation, and economic incentive must have been pretty high to drive people to over come all of these factors.

Much of the important points have been hit already, but I wanted to note that Africa was in fact not colonized "on a wide scale" until the mid 19th-century. The first volume of the UNESCO History of Africa series has a good essay on the causes. In addition to disease and the lack of significant military advantage, the question of motive is important. To a significant degree, it's the desire for specific resources provoked by the Industrial Revolution in Europe that motivates European powers to claim territories in the African interior, as opposed to the small coastal zones that had been claimed during the era of the slave trade.

Northern Africa has been colonized for centuries by Arabs. Need to get past them first.

When you have guys like the Barbary Pirates terrorizing the Mediterranean and West African coasts, there is not much incentive or possibility to start a huge colonization project.