I believe after Ben and the Others took over from Dharma, Ben made a deal with Dharma to run the island, or at least hold control of the island. When Ben cut off communication with the outside world, which happened after the plane crashed since the Others did see information about the plane from the outside world, Dharma decided to come and see what was up and get Ben.
[The freighter people] are either there to retake the island or at least to determine what is going on with Ben and the Others. The other indication that they are Dharma is that Ben had an ally on the boat that he could not have had unless he knew who they were, and thus we are back to the Dharma and Ben deal to look after the island.
Dharma definitely exists in the outside world as food drops kept happening from Dharma when the survivors were on the island. Dharma are also the ones that must have collected the information on the survivors that Ben keeps using. The others with Ben are island bound so the only help they could get are from people who knew of the island and the submarine.
Also it was funny that Ms. Lewis who was the person shot by Ben, smiled when she saw the polar bear Dharma collar in the desert. Knowing she was in Dharma or hired by them would make anyone smile.
What do you think of Dizzy Dan's Dharma Freighters theory? Discuss in the About Lost forums: Dharma Freighters theory.
