This question obviously comes with all the complications of Africa being an extremely large and varied continent, and instead of attempting to provide an overview of the whole continent I'll just post one passage that will answer the question of whether homosexuality was tolerated at any place on the continent.

In the c. 1590 the English traveller Andrew Battel travelled through Angola, and spent some time observing the Imbangala, who were essentially at the time known as quite a brutal tribe of marauders who were reputed to practice customs such as human sacrifice, cannibalism and torture. Battel wrote:

The men of this place wear skins about their middles, and beads about their necks. They carry darts of iron, and bow and arrows in their hands. They are beastly in their living, for they have men in women's(62) apparel, whom they keep among their wives. [(source)](http://www.erbzine.com/mag18/battell.htm#(62)

It seems that what is being portrayed here is a tribal structure that is relatively similar to those observed in indigenous communities in the Americas; homosexuality in its current strictures cannot truly be applied, but the adoption of a traditionally female role by a male was certainly an element of pre-colonial African tribal society.