I didn't know this was news. I and other security researchers & law enforcement have known about it for a while. I assisted in one court case where the data was used as evidence. I suspect the slick-looking iPhoneTracker app finally made it interesting to the media. Edit: There was a similar deal on iOS 3 but it seemed more like a bug, not a feature. Data would be purged at some unpredictable interval. I can't recall…
Apple acknowledged that to the House of Representatives. They're gathering data about their customers, including GPS : [PDF] http://markey.house.gov/docs/applemarkeybarton7-12-10.pdf
II / C / 1 / a. : "Second, to help Apple update and maintain its database with known location information, Apple may also collect and transmit Cell Tower and Wi-Fi Access Point Information automatically. With one exception, Apple automatically collects this information only if the device’s location-based service capabilities are toggled to “On” and the customer uses an application requiring location-based infomiation. If both conditions are met, the device intermittently and anonymously collects Cell Tower and Wi-Fi Access Point Information from the cell towers and Wi-Fi access points that it can “see”, along with the device’s GPS coordinates, if available. This information is batched and then encrypted and transmitted to Apple over a Wi-Fi Internet connection every twelve hours (or later if the device does not have Wi-Fi Intemet access at that time)."