VLC is not recommended at all as it uses direct AirPlay, meaning horrendous image quality / framerate.
If you do want to play back MKV's from an iOS device without remuxing and over AirPlay, currently the only one way to go is Infuse. (The iOS6-compliant 1.5.x will do, you won't necessarily need v2, which is iOS7-only.)
Exactly. Only the native mode of AirPlay should be used, which can only be done via iOS-native media files (mp4 / m4v / mov) or Infuse's MKV / MTS support.