This is a personal reason, but the reason I prefer case sensitive directory names is I can make "logical groupings" for things. So, my python git directory might have "Projects/" and "Packages/," and the capitalization not only makes them stand out as a sort of "root path" for whatever's underneath, but the capitalization makes me conscious of the commands I'm typing with that path. I can't just autopilot a path name, I have to consciously hit shift when tab completion stops working.
That might sound like a dumb reason, but it's kept me from moving things into the wrong directory, or accidentally removing a directory multiple times in the past.
I also use Windows regularly and it really isn't a hindrance, so maybe I wouldn't actually be bothered if everything was case sensitive.