I thought the answer to this question was kind of obvious. The Cylons don't want to wipe out humanity. They are interested in herding them to some goal or destination. Look at the facts:
(1) The Cylons can get agents on board human ships. They've done it multiple times.
(2) The Cylons, by corollary, seem to know where the humans are on a regular basis.
(3) The Cylon ships are better than human ships, they can jump straight from Caprica to the Galatica's current location.
(4) The Helo-Boomer subplot makes clear that Six and her cohorts are driving Helo in a particular direction, and, if he doesn't take the path they have laid out for him, they will kill him.
(5) The Galactica seems to be being guided as well, given the location that various Cylons have appeared near it.
The Cylons are herding the humans. Apparently Galactica to Cobol (and my guess is Helo to the arrow of Apollo). They need the humans to do something. Perhaps breaking a cycle that has happened before (remember the cyclical nature of history everyone keeps talking about).
Think about this: if Cobol is the place where the humans and Gods lived in peace, who were the Gods? Think about the cyclical nature of history - this has all happened before. Now think who the humans might currently want to live in peace with.