The ports are all Thunderbolt 3 ports, which I believe by definition means they are USB 3.1 ports as well. But some devices out in the world have USB-C ports that are not Thunderbolt 3 compatible. No longer can you tell what sort of devices will work with a port by its physical shape. For instance, I have a Windows desktop machine with a single USB-C port on the back, but it's not a Thunderbolt 3 port. So while I could physically plug in a Thunderbolt 3-only device, it wouldn't function at all.
Thunderbolt 3 is backward compatible with Thunderbolt 1/2 via an adapter, but the Thunderbolt 2 adapter that Apple sells does not function identically to a Thunderbolt 2 port on previous generation Macs - e.g. you cannot plug a Mini DisplayPort display into it. Thunderbolt displays do work with it though.
Also, the lower-end 12" MacBook that Apple sells with a single USB-C port is NOT a Thunderbolt 3 port, so you have to know which devices that have identical connectors will work with it. Apple makes the distinction on its peripherals by screenprinting a little Thunderbolt logo onto the cable/connector housing. The messaging was reinforced with corresponding Thunderbolt logos next to the connectors on previous iterations of the MacBooks - making it obvious that these ports were not just Mini DisplayPorts but also Thunderbolt ports - but the new 2016 models don't appear to have anything like that on the hardware.
Additionally, there are USB-C cables and Thunderbolt 3 cables. Thunderbolt 3 cables are apparently higher-spec and will always work as USB-C cables, but the opposite is not necessarily true.