Yes, it only looks at public repositories. It wouldn't be hard to look at private ones but it would require the user to OAuth so the app has access. But I'm not sure if Github supports using OAuth entirely in Javascript (like https://developers.geoloqi.com/client-libraries/Javascript) so then it would require a server-side backend to handle the login.

I'd imagine that with most paid accounts the private repos are also the largest. I know my stats would we be completely different if it included those.