Tragedy in a southern church full of African Americans takes us (and especially the media) back in our minds to a time when such places were bombed or torched by white men with sheets on their heads. It cries of hatred. Churches get more sympathy in the media because of the ideal that they are places where, as Barack Obama said, people seek solice and peace.
This article that sir82 linked is very fair about it. We imagine that such places are set apart from other spheres in life and when we hear about tragedies, we think how that is so much hatred against such innocent people. But of course that isn't typically true as black churches (and others) are often political centers that would make them more valuable targets in any hatred wars than any campaign offices.
Politicians must be the slicksters they are and put these tragedies right up there with school shootings, and to be fair, there are typically plenty of innocent children in the church. The media will always be over-the-top.
Besides neighborhoods, churches and schools are the main place where segregation is the norm. Charleston has a history of banning blacks from Christian churches even though the white people in them had a hand in converting the blacks to begin with, so churches of their own were formed by blacks and they have tended to stay segregated all these years later.
Well, a white man might really stand out in a black neighborhood and put people on guard so that he may not be able to kill so many. But people in a church might just think he's another Christian that didn't realize how much he stands out.