"They come, they fight, they destroy, they corrupt. It always ends the same." So the Man in Black says to Jacob. But who are "they"? Does he mean humanity in general, or one group in particular?
If LOST is really about our characters, and they're tied into the destiny of the Island, and that destiny couldn't be revealed until the end, I think it's because of Jacob and the Man in Black. How are the Losties tied to the demigods of the Island? Well, they're family.
Why hide the Man in Black's true name? Because his true name is AARON. He took the form of Locke, his metaphorical grandfather, the man who built him his cradle. He's a liar and a manipulator---as a baby, Aaron was lulled to sleep by the voice of Sawyer, the con man, and was raised for a time by Kate, the fugitive. His go-to babysitter was Sun, and he escaped the Island because of Frank---two people whom the MIB for some reason really wanted to hang around with.
I think sometime in the last three years, Claire had another baby (Charlie's kid, perhaps?), and that baby is Jacob. That's why Claire ended up in the cabin---she couldn't head back in time with the rest because Jacob needed to be born at a certain time. Jacob "spoke through" Christian, his grandfather (and I think Christian really did represent Jacob---white shoes vs black shoes).
Through the time-and-reality-shifting energies of the Island, these two brothers essentially became demigods. And here is the heart of their quarrel: rebirth and family. Their 'family' is constantly reborn, constantly reincarnated, and Jacob keeps bringing them to the Island, where they fight, destroy, and corrupt. Aaron wants to release them from this endless cycle, but Jacob is lonely and hopes that their mother, uncle, and all the people who raised them (Sawyer, Kate, Hurley, etc.) will eventually be able to break the cycle of violence and live peacefully with them on the Island.
Dogen was shocked by Jacob's note. We know it had a list of names and an instruction to save Sayid, but was that really it? The Others are suddenly desperate to protect the Losties, the Temple guards step aside at Jack's say-so, and the Others are either unable or too afraid to kill Sayid. Why? And what did Justin mean when he said Jin couldn't be harmed because he was "one of them"?
I think the note told Dogen who these people really are---they're Jacob's family, who have ruled on the Island before and will rule again. (I don't think the Others know the true nature of Jacob/MIB's relationship.) During the 'pill scene' in What Kate Does, Dogen seemed pained at being unable to tell Jack what was going on. He told Jack he'd been brought to the Island, and that Jack "knew exactly what [he] mean[s]." I think Dogen has met Jack and the rest before, and Jacob's note jogged his memory (just as Sawyer's "did you bury the bomb?" did to Richard).
Maybe the Losties, along with Richard, were prisoners on the Black Rock, and Richard lost his memories of them when he took a bath in the Temple Spring? Maybe Dharma was targeted for extermination because of their rejection of the Losties in their midst.