We are launching a new version of the updater for Linux later today that sets the necessary permissions automatically. However, the newest version of the game has a problem on Linux, where the sound system crashes, so we are investigating this as well.
Viewing post in 0.6.0.2 - Self-update launcher comments
The Linux patcher is up and running, but the game is still broken for Linux users. FMOD, the music system we're using, has a bug with the version of Unity we're using for Linux, and they have fixed it in their newest version. We're going to upgrade the the newest FMOD version tomorrow and will upload a new Linux build then.