Wikipedia says: "Sam Lantinga created the library, first releasing it in early 1998, while working for Loki Software. He got the idea while porting a Windows application to Macintosh."
Even the naming of directmedia suggests microsoft roots to me: direct3d directplay directx, etc.
But my larger point was that I don't know how you would create a "native linux" game - I think high-functioning games on linux use cross-platform toolkits of one type or another.
I don't know maybe you could cobble something together part wayland, part mesa, part pulseaudio, part v4l, part /dev/input...
You could make a distinction for Windows/whatever games bundled together without Wine/eON/whatever and depending what want to determine that might make sense but at that point you probably also want to exclude things like Unity that don't really do a great job at integreating into the Linux environment.
SDL can be used for porting games (ie, making them native) and that's what it was originally created for but it's not really comparable to bundling a Windows .exe with Wine, which would add a lot more complexity.
Huh?
Building on top of SDL is probably the easiest way to make a game native on all platforms. There's nothing Windows specific about it.