You misunderstood that. There is no compatibility as USB-C is the connector Thunderbolt will use with version 3. Version 1 and 2 use a connector that is not only similar to mini DisplayPort but also compatible with it. This difference in connectors will require the use of an adapter for those with a Thunderbolt 3 Mac but Thunderbolt 1 and/or 2 devices.
Intel went 1 step further but Thunderbolt 3 by not only using the USB-C connector but also by including USB3.1 Gen1 & 2. That makes the Thunderbolt 3 port not only "speak" Thunderbolt but also USB. This is a necessity in order to reduce the confusion we're going to get somewhat. We'll still have some as Thunderbolt 3 devices can physically connect to a USB port that uses the USB-C connector but it cannot communicate with it (USB does not do Thunderbolt). Because of Thunderbolt 3 also supporting USB there is no need for USB-C adapters as there already are a few. What we need with Thunderbolt 3 are adapters to connect Thunderbolt 1 and 2 devices.
Read up on both USB and Thunderbolt, you are lacking a lot of knowledge concerning those two protocols. Apple, like others, uses the USB-C port on a device that is not targeted at power users for the mere fact that USB isn't targeted at power users. Thunderbolt is a high end technology aimed at power users and thus can be found in computers and motherboards targeted at that specific audience (=power users).
The MacBook is not only targeted at normal users, it is specifically targeted at normal users requiring mobility and simplicity. For them that 1 port is of more use than the amount of ports on the MacBook Pro series. From a technical point of view, Thunderbolt is not even possible on the MacBook because of internal dimensions which is the exact same reason why there isn't USB 3.1 Gen 2 support. Both require a separate chip on the PCB and there simply isn't room for it. This will change when Intel integrates the Thunderbolt controller into the CPU (they are working on that). Does that all matter? Nope, the target audience doesn't require it. Most of them only use the power cable, they don't really connect anything to it (well, maybe a bluetooth mouse). Most people don't have Thunderbolt devices because of the price (take a look at all the Thunderbolt news items here; you're going to find a lot of posts that state Thunderbolt is too expensive). The only thing that audience is going to connect is a dockingstation. There are many USB dockingstations on the market and now there are also ones with the USB-C connector.
This is just Apple creating a notebook with a standard port for a very specific audience and that audience is perfectly fine with having that 1 port and it being USB-C. But boy, do I wish for a MacBook with more computing power and Thunderbolt 3, that would be sweet!