I quite dislike and don't get the point about them being atheists. What's the connection?

The connection is that the whole point of Phil Robertson's spiel was a criticism of atheism and atheists, the idea being that because atheists can't get their moral values from God they don't, or shouldn't, or can't coherently, have moral values at all (and, allegedly, therefore aren't in a position to complain if their family is abused and murdered and they are mutilated).

That's all kinds of wrong, and Scott understands that; the only thing he's defending is one specific feature of Robertson's crappy argument that some people have taken offence at, namely its use of an unpleasant thought experiment in which awful things are done to an atheist and his family.