They were protesting all that nasty shit going on in Darfur, a region in Western Sudan. In case you forgot, there was a 20 year civil war in Sudan:

But that’s not really why Clooney got himself arrested. The fighting [...] has largely subsided. The Sudanese government has basically won. Now, they are punishing the civilians who still live in the Nuba Mountain border regions by blocking humanitarian access to the region. The Sudanese government is not letting groups like the World Food Program, UN Refugee Agency, or Red Cross/Red Crescent bring food or medicine to people in the region. The UN is warning of a looming famine and mass starvation in the Nuba Mountain region of Sudan. About 200,000 people on the Sudanese side of the border are at immediate risk of starvation.

Now you know.