[MiamiSpartan]

While I think there are definite Dharma elements on the ship (maybe even remnants with a different organization), there are a few things that need explaining:
1) If the Dharma people back home know what Ben did to their people, why did the food drops continue?
2) If Dharma could find the island to drop the food, why couldn't they find the island at any other point for this revenge mission against Ben? Even if they are only having trouble finding the island after the hatch blew up, why did they never go after Ben before that?
3) How did Dharma know about Desmond/Penny? A strong possibility is if Widmore is involved with Dharma, but it still doesn't answer some other questions.
4) How would Dharma know about the survivors? Another clear indication that whoever is on the boat DOES know about the survivors is that it doesn't make sense to send Naomi onto the island to find one person (Desmond) while avoiding everyone else (the Others). It's a lot easier to find a sizeable group (the Losties).
5) Why does the Island tell Locke that these people are a danger to the Losties?

All this adds up to two possibilites. Either Ben is not the REAL mission of these Dharma folks, or it is not a Dharma-run operation at all, but perhaps with some former Dharma people involved.