I am not that familiar with the details in those regions but what is true is they all have large western christian missionary groups and are newly christianized groups (during colonialism). They are most protestant evangelicals, who are pro-zionist, anti-Muslim by nature so close ties to the west/zionists and are taught to fear/hate Islam and its growth.
The South Sudanese have been through war, so for some they probably associate it with that, but many are also Muslim.
Nigerians are known to be evangelicals who hate Islam and Muslims.
Kenyans on the other hand generally seem to be unproblematic but there is a clear push the past few years, what mostly looks to be an online campaign and some videos coming out of their churches, to direct hate towards Islam and Somalis.
It is also important to clarify when I say "Nigerians" for example, Nigeria is a majority Muslim country. The Majority Muslim population was marginalized and the southern new christianized and westernized non Muslim groups were of course favoured by the colonizers and empowered.
As Islam continue to grow in the country a lot of the evangelical western propped up southern Nigerians have resorted to islamophobia and hatred.
There is a significant Muslim population in South Sudan as well. It is said to be 6-7% and growing.
We are more familiar with Kenya, and anyone who has been there will notice how large to the Muslim population is even outside of Somalis. Even then, they claim Muslims are only 10%.
I think the Muslim population in all of these countries including Ethiopia is a lot larger then they admit, they are probably hiding the true numbers.
Similiar to France and Europe, when islamophobia spikes and they panic and start attacking Muslims, it usually means the population is growing and becoming more religious, and not secularized like they had originally hoped.