Apple introduced USB-C to its user base with the retina 12-inch MacBook. At the time, it was a fancy USB port limited to USB 3.0 speeds of 5Gbit per second, and was officially called USB 3.1 Type-C Generation 1.
The same physical port was used in the 2016 MacBook Pro refresh, offering a faster, more capable Thunderbolt 3 port with the same USB-C physical connector. The Thunderbolt 3 protocol allows for 40Gbit per second —assuming the cabling for it is right.
But, right now, confusion reigns —and a simple choice that Apple made in the 2016 MacBook Pro is making it worse.