I think these are actually the most minor problems with the USB-C vision. The VAST majority of consumers will never encounter a thunderbolt device, and the ones that do can be expected to understand the cable difference.
What is far more of an issue for the standard is the established network effect. USB-A has become so commonplace that its built into our furniture, and micro-USB is a legally defined requirement for device charging in some areas. These foundational forces will prove to be a massive deterrent to USB-C uptake, and far more of a risk to the vision than multiple cable types that are clearly labeled!
But, the bright side of this I think is Apple's adoption of the Qi charging standard. Its clear that an evolutional jump to wireless charging will entail new technology, so I see Qi taking up the "one way to charge everything" vision.
What is far more of an issue for the standard is the established network effect. USB-A has become so commonplace that its built into our furniture, and micro-USB is a legally defined requirement for device charging in some areas. These foundational forces will prove to be a massive deterrent to USB-C uptake, and far more of a risk to the vision than multiple cable types that are clearly labeled!
But, the bright side of this I think is Apple's adoption of the Qi charging standard. Its clear that an evolutional jump to wireless charging will entail new technology, so I see Qi taking up the "one way to charge everything" vision.