Well it is likely that literacy in Arabic script was initially mostly the province of the religious class and it was long considered necessary for proper religious writing to be in Arabic.
But that aside, my understanding is that at least a few languages were being written in Arabic script by the time of the European conquest. The Hausa were literate in Arabic from the 15th century and by at least the early 19th Hausa itself was being written in Ajami, an adaptation of Arabic script ( remember they weren’t brought under European control until the late 19th ). I believe Swahili literature dates back even further, to the early 18th.
The biggest factor was probably time - the diffusion of literacy in Africa just happened late in history. Had it occurred a few centuries earlier, native scripts might have been much more common.
- Tamerlane