Steam survey shows Linux marketshare hitting 1.0%
Some problems mentioned on the comments on here, although I can think of other problems too than only the ones mentioned. So, I can think of another possible solution to these and many other problems (although it has limitations, but there always will be): Don't design your game for Windows or Linux; write it for Famicom or Game Boy Advance or whatever (or design your own open source VM if you must, and use that). Emulators are available for many computer systems (including the less common ones), and will do many things for you automatically too that you will not have to deal with by yourself, such as rebinding controls, zoom levels, etc. They will then also the user will not have to worry about malware as much, either.