Agreed, all ports are USB's but not all ports are thunderbolts.
I guess from Apple's standpoint, if you're competent enough to know you need the speed of the thunderbolt device, you're also competent enough to know which port is which.
Actually I take that back, it's going to be a nightmare for new Thunderbolt displays, which many normal users will buy.
I think the point is that its not two technologies being merged, more that USB-C was also developed to be nothing more than a port shape.
The issue here is the marketing, the fact its called "USB"-c will confuse everyone, that was a silly name, they should have just given it another name totally separate from a protocol that could run through it as thats instantly going to confuse most tech users, including those on this forum no doubt. Secondly, they should have made even more fuss about it just being a PORT not a connection protocol. To be fair they have made that distinction quite a few times but no one was really listening and assumed this was just all USB 3+
The beauty here, or the intention is that you should have one port, multiple protocols. Thunderbolt. Displayport, USB, HDMI, DVI, PCI-E, all running through the same connection. Apple will simplify things in their next rMBP line in that all available ports will be Thunderbolt 3 and USB3.1 in a USB-C adapter. Whatever device you buy will be compatible. Its just when people start buying Thunderbolt 3 devices for their 12" Retina Macbook because "the port looks the same" that trouble starts...
...long term, one port to replace HDMI, displayport, USB type A. Id be happy to keep magsafe for charging though - I think people wanting SD card slots should probably accept they need to use dongles though, seems a luxury having such a slow port built in to connect to the USB bus.