This is more of a success for people who write DRM-bypassing software such as Cydia (iPhone) or Handbrake (Mac DVD). Prior to this ruling, they were subject to the wrath of Apple, MPAA, etc because they were actively distributing software that violated the DMCA. Users were rarely bothered in comparison.
That said, there is nothing preventing Apple from declaring all warrantees void if the operating system is altered. My Subaru warrantee is similar: if I modify my engine, I void the warrantee on that part or whole of the engine.
Also, there is nothing preventing AT&T from modifying or enforcing a service contract terms prohibiting VOIP or tethering or another use of data services they wish to prevent.
As for who “owns” the iPhone: you own the hardware, but Apple owns the software and licenses it to you for a fee paid when you purchase your phone. As another poster mentioned, often the price of your phone was subsidized by the carrier who may enforce the term of the contract if you decide to leave.