They began using the Lightning connector 2 years before USB-C was a thing. They have a long term support philosophy and they stand by lightning. Perhaps in the future they deem the adoption rate of USB-C good enough to use that, but until then they'll keep using Lightning.
Because of all the docks and alarm clocks that still only expose a lightning port.
It will be super easy to support the USB-C Macbooks out of box -- they just swap out the USB-A-to-lightning cable and charger in the box with a USB-C-to-lightning cable and charger.
That's not really a great reason - there were lots of alarm clocks and docks with the 30-pin connector (and still are if you go to a Hotel!). That said, I'm not sure why Apple went with Lightning for their mobile devices instead of USB-C - maybe timing?