I don't think WB is scared of Wonder Woman; I think they're just scared of super heroes in general. The feature film division of WB doesn't "get it"; I imagine their meetings are a lot like Wall Street tycoons trying to plot the next My Little Pony episode. I envision a few moments of awkward silence and then a grey haired suit exclaiming "What is this shit?" just before he demands a glass of scotch.
I believe WB has had success by luck on their super hero feature films. It was the happenstance that Donner, Burton and Nolan were interested; that's all. WB doesn't know good from bad on this stuff; they are absolutely befuddled by it. They finally just pick something like pulling the handle on the slot machine and then see what come up.