I know what it's all about.
It's suddenly clear
It's about The Island.
Well, yes, you say, and maybe "duh", but surely now it's obvious. The rescue crew from the helicopter work for The Dharma Initiative, or rather that Hanso bloke who is behind the Dharma stuff. They're a bit annoyed with Ben because he killed them all then cloaked the island. It's taken them this long to find the island again. The crashing plane was the clue. (Although not entirely sure how they managed to parachute in Naomi in the first place.)
So, the survivors of Oceanic Flight 815 are a mere nuisance, hence the big cover up.
I enjoyed the mutliple person flashbacks this episode. Well, actually, as usual, I enjoyed everything about it. Lost is currently my favourite thing on TV by a huge margin.
Unless it really is the Island... in the sense that the Island has developed some form of sentience, in a concentrated Gaia-theory kinda way...
I agree that the Dharma folks would want to sort Ben out and that he might have set up some form of cloaking device (big magnetic fields and all that), but then why did they send an archaeologist, a physicist and a ghost-whisperer, with only a pilot and a single bodyguard as backup, rather than a full combat team..?
Because a full combat team would have really dull flashbacks!