This is from the official Thunderbolt website:
"
@dustbeta asks: Will Thunderbolt 3 require special USB Type-C cables? Or will any Type-C cable work?
Any USB Type-C cable will work in a Thunderbolt 3 port. However, connecting to a Thunderbolt 3 device will require a Thunderbolt cable.
"
Sauce: https://thunderbolttechnology.net/blog/you-tweeted-we-listened-thunderbolt-3-capabilities-and-more
Ah, that's right. I forgot that Thunderbolt requires a chip in the cable itself. So there will indeed be USB-C cables that will or will not handle Thunderbolt 3. Kind of a nightmare for those no aquainted with all the protocols going into one connector. But I could see where, within a couple of years, every USB-C cable will just automatically include all the protocols, unless there's still a large cost between including it or leaving it out.