Um, the linked article says "no suggestion that [Apple] has been uploading or using the information."

According to some reports, it is a cache of cell tower locations, used internally by the device either to speed up acquisition of GPS lock, or else provide location-based services in the absence of GPS. Storing the data on the device avoids network traffic, and incidentally gives Apple less information than if it asked their servers every time.

I'm not yet sure which reports to believe. A key question is whether it accumulates multiple entries per cell tower; some reports say it doesn't, and that new entries overwrite old ones. It does seem like the researchers who announced this and got the recent publicity, didn't do due diligence because it was already well-known. There have even been books published about it.

And it does sound like Apple don't have any sinister motivation. The data is on your phone and they don't get to see it. (It may still be a security risk, though.)