The continent's security is hampered by its sheer size and the massive borders of many of its countries. What this means it that few countries have the funds for large and capable enough security forces to exercise control over the whole of their territory. So outside the cities, large parts of the countryside exist in a security vacuum where thugs, rebels, criminals and assorted other unsavoury types essentially have free reign.
It also hampers trade and communication. With communities being spread out over such huge distances, transport infrastructure and the associated costs become vital. But few African nations can afford to maintain proper highway networks and even if they could, there's a lack of sufficient transport capability to effectively utilise it. As a result, intra-state trade is severely limited and inter-state trade even more so. This logistics problem also affects the delivery of aid.
To be fair, this isn't true of all African countries. South Africa and Egypt, for example, are notable exceptions for having a security presence throughout the country, a well-developed and advanced transport infrastructure and so on. But bringing countries like the DRC, CAR & Uganda up to the same level is not going to be an easy task.
One hope lies in having less of a top-down socialist central-planning approach and more encouragement of a federal self-organising entrepreneurial environment to encourage communities to grow themselves and gradually build their own transport and communications networks outwards. Technology will make this easier, but I think anybody expecting an economic revolution in Africa anytime soon is holding on to a false hope.