Motherboards that don't work with Linux

So, my father has a small PC repair business and likes to build PCs. He and I were talking today and he mentioned that he finds motherboards all the time that aren't compatible with Linux operating systems. Looking at the buyer reviews, whenever there is a low rating due to this with a manufacturer response, it's something along the lines of "we don't support non-traditional [ie open-source] operating systems."

Does anyone here know exactly why this is? Is there some shady anti-trust stuff going on, or is there some issue I'm not aware of with making hardware compatible with a Linux-based OS?