Why not? But attacking a religion wasn't his (own) motive - from what I've read, he wanted to start another race war. His actions were racially motivated. (However, his decision to attack a church, rather than other areas, may have been motivated by other means. Your observation about the civil rights movement is probably an accurate one. You have to wonder, though... what made the churches significant during that particular time? Was it because it was the best place for blacks to gather? Or was there something else going on - some inspiration from another source, as it were? )Let me reverse the question on you: If it wasn't a racial attack, then why not attack a white church? Or a megachurch?
Now, if someone was motivated by a hatred of another faith, I could see them targeting megachurches or what have you. We have certainly seen this kind of thing in other countries. It hasn't happened here yet, and let's hope it doesn't. Actually, scratch that - let's make sure it doesn't happen here by preventing it in the first place. I think this would be best served through open and honest dialogue and an adjustment in our way of thinking. We need to move beyond the idea that just because someone has a different ideology that automatically makes them an enemy. This kind of sharp division has been growing more and more in recent years - the above dismissed lawsuit may be a minor example, but who's to say what will happen when it occurs again?