Since when is a commuter flight in the US a code share flight. Just because the flight is outsourced, it is in every other regard the owning carrier flight.
eg. the flight I referenced above - you cannot buy tickets on Skywest airlines. It is sold as a Delta flight, the only flight number is a Delta flight. Saying it is a code share and therefore not able to earn points cuts out half of the flights on the Delta network.
A truely codeshare flight eg. Olympic is understandable, but excluding the outsourced flights is just down right madness, and these flights earn points in the Star Alliance, Skyteam and One World Schemes.
If Virgin truely want Velocity to be a rival for Air New Zealand Airpoints or Qantas Frequent Flyer, then refusing to count outsourced flights will drive away the true Frequent Flyers that fly globally, and spend a lot on flights.