“Apple’s goal has always been to insure that our customers have a great experience with their iPhone and we know that jailbreaking can severely degrade the experience. As we’ve said before, the vast majority of customers do not jailbreak their iPhones as this can violate the warranty and can cause the iPhone to become unstable and not work reliably.”
Basically while jailbreaking is now legal as long as its not used to obtain illegal items, Apple still frowns on this and will void your warranty. While it is true that you will probably have the best experience with the phone with its factory software on it, but we still should be able to do whatever we want with the hardware, however I do agree that it should violate your warranty if you modify the software outside the warranty's terms.
Other source: http://www.cultofmac.com/apples-official-response-to-dmca-jailbreak-exemption-it-voids-your-warranty/52463