It has terrible default orphan/widow control, and editing anything graphical is a royal pain in the ass: the slightest wrong touch can throw your diagram into disarray. Those that "know" how to use it I've noticed seem to have near-infinite patience and knowledge of where all of Word's "land mines" are and how to avoid them.
People use it because it bundles in every obscure feature under the sun, so it's effectively the lowest common denominator when it comes to meeting an organizations' needs. And for those who already know how to use it, I suspect the sunk cost fallacy keeps them there.