I can understand that OS X probably has the biggest share of GitHub visitors, but git is fully open source, GitHub seem to very much like open source, and in the spirit of that I'd expect a native app that works on as many platforms as possible.
The definition of native app has changed. It's no longer a synonym for compiled binary; or using native widget. It is not as simple as coding your UI in a cross-platform toolkit. In these days, a native app means something that feels like the built-in apps: it's beyond skinning and appearance and is more about how the app as a whole interacts with the user to get the job done. As the platforms diverge, it's now really hard - if not impossible - to make a cross-platform native app. Among Performance, Cost, Time, Scope, you can only pick three. GitHub sacrifices the scope.
Apparently, GitHub chose to do best they can for one platform instead of something that is merely good enough on few platforms.
Sure you can build cross-platform stuff using Java or QT, but has anyone actually liked the stuff that came out from that?