The iPhone is NOT the flagship product, and it is not part of the iPod lineup. If you look at what products Apple actually moves- they sells far more iPod nanos then any other product they offer. It only makes sense for them to push it to the forefront of their iPod lineup.
Also, the “Let’s Rock” event was an iPod/iTunes event. That’s why they focused on their announcements regarding those products.
That being said, they have already stated that they will bring the Genius playlist functionality to the iPhone with the 2.1 update.
And P.S. – Apple no longer makes a monthly income stream on the iPhone. That part of their agreement with AT&T has been restructured, which is why the iPhone 3G is so much less expensive then the iPhone 2G was- because Apple relinquished those monthly kickbacks in favor of a more traditional lump subsidy payment.