This connection between thoughts and devices is already happening, albeit discretely, and in an assisted way, allowing paralyzed people to steer their wheelchairs or direct robotic arms using only their thoughts.
The natural evolution of this is that this mind-machine technology follows Moore's Law, and gets better, faster, cheaper and smaller. Eventually it makes it onto our phones, or is embedded in a Facebook powered Oculus Rift.
To me, then, the question that Apple is (currently) considering as it opposes the FBI's demand to decrypt and provide access to the San Bernadino murderer's iPhone is:
"Will people trust us with protecting their thoughts when our iPhones are an extension of our minds?"
To me, Apple is protecting its world class brand, while also thinking of the larger implications of the government's requests for private, personal information which is increasingly blurred with the realm of personal thought.
If it were possible today for the FBI to read our minds, which are currently encrypted in their own way, would we accept the FBI's request for a "backdoor" in order to do so?
To me, the answer is obvious. As the human mind becomes more connected, both controlling and being controlled, by digital communication, the future all of our communications will, and should, be encrypted. This will be by default to protect individual privacy as much as possible.
Whether Apple ends up losing the battle with the FBI or not, Apple is doing the smart thing by objecting to the court order and representing the current and future privacy rights of individuals in this battle.