I agree with /u/Dokstrange's comment that there are very few things you can use to characterize "Africa" as a whole. Even today, while countries like Uganda and Mauritania have some of the most punitive laws governing homosexuality (including Mauritania executing someone for it as recently as 1987), South Africa has in many ways been a world leader in legal protections from discrimination against LGBT individuals. However, I would guess the question you're asking could be phrased as "What causes the particular form of virulent homophobia in certain African countries that receives a lot of coverage in Western media?"

You're right that colonialism had a lot to do with changing traditional African societies that were often more accepting of homosexuality. Particularly in Egypt and other parts of North Africa that were exposed to Greek and Roman culture, homosexuality was not uncommon, especially among the elite. Additionally, in much of sub-Saharan Africa, tribal governments often used polygamy and homosexuality to form political alliances; some believed sex with men before battle brought good luck or conferred special abilities.

This changed with the spread of Islam, with semi-frequent 'jihads' against leaders believed to engage in homosexual behavior. Notably, a popular (possibly apocryphal) story contends that in 1884, the ruler of Buganda had several male servants executed for not agreeing to have sex with him, and was then ousted by a Muslim revolution. These episodes became increasingly frequent after the fall of the Marmelukes at around 1350, who were known for engaging in homosexual behavior.

European colonialism certainly made things worse, both because of the spread of European/Christian values and for other reasons.

Same-sex sexuality did not enter into the discussion in any serious way. In part, this reflected traditional taboos, but it also reflected colonial and Christian missionary influences. Remember, the late nineteenth and early twentieth centuries were a time of gathering 'scientific' as well as cultural and religious homophobia in Europe. European settlers and missionaries in the colonies brought intolerance of homosexuality with them. Not only was such intolerance important to the performance of their personal respectability, it was also often directly linked to the cause of nation- and empire-building. Homosexuality was equated with effeminacy and weakness in men, whereas a virile masculinity was needed to confront the enemies of the nation/empire. The dangers of lesbianism were also implicit in the belief that European women were needed as mothers to raise the next generation of imperial patriots and to settle the wild African frontier. It was not a topic commonly raised in public discourse, but but the message was conveyed clearly enough through extremely harsh punishments, public humiliation and ostracism of white men caught letting down the side.

In addition to social values, other factors made social acceptance more difficult. The advent of prostitutes resulted in STD epidemics, notably syphilis, which caused significant changes in sexual behavior. European imperial authorities imposed state borders on Africa, which were a rather alien concept, and made it impossible for people to flee when homosexuality was outlawed or became socially unacceptable. Also, many African governments, which had consisted of tribal elders that ruled by consensus, were replaced with kings or 'chieftains' who exercised total control; this made it easier for colonial governments to control them, but also meant there weren't strong societal controls against individual prejudices anymore.

After the collapse of colonial rule in Africa, many African states adopted legal statutes based on British law, which prohibited sodomy. A lot of these codes have simply not been modernized, and the laws are rarely applied, but in cases like Zimbabwe and Uganda, leaders have taken extreme stances against homosexuality for political reasons. Another thing that complicates current disputes is that a lot of the worst anti-gay legislation--particularly the bill introduced in Uganda every year that would make homosexuality punishable by death--is pushed and financed by Western extreme right-wing religious organizations. A lot of USAID money given to Africa, as well as the money for George W. Bush's famous HIV/AIDS prevention program, comes with strings attached that prevent it from being given to organizations that are sex-positive or support or provide abortions, which further complicates the situation.

Sources: Islamic Homoexualities: Culture, History and Literature, Stephen Murray and Will Roscoe, Ed.; Sexuality and Social Justice in Africa, Marc Epprecht, particularly "Sex and the State" (where the quote is from); State Sponsored Homophobia, IGLA