I have only ever seen one control system that did not use windows for the HMI. It was back in 2002 at a electric distribution utility their SCADA system ran on a DEC Alpha with some kind of unix. I've been to 30+ power plants since then, all windows. I deployed linux to 3 power plants and it was a pain in the ass because nobody knew anything about maintaining linux in the remote areas where the power plants were.
All of the PLC programming software from the big manufacturers runs on windows. this is reality.