Several reasons.
a) Intel wants licensing cash for allowing you to use it
b) It does not actually add that much to USB. You want to attach monitors? Non-Thunderbolt USB can do that. You want to attach storage? Non-Thunderbolt USB can do that. Networking? Charge your device? USB can do all that.
The remaining selling point of Thunderbolt is that you can attach an external graphics card over it. There are external USB graphics solutions, too, but they can't really compete if you plan to do high perf 3d graphics over it.
However this selling point is also the Achilles heel of Thunderbold. It exposes PCIe to devices outside the device, allowing direct memory access over it. This can be partially mitigated if the OS and all drivers cooperate and are really well written (for example not expose a memory page that contains other stuff as well).
But bottom line? I actually view this as an AMD advantage. It's a bit like Firewire was. a) it cost licensing money and b) it introduced a similar security issue while c) not actually delivering that much of an advantage over USB unless you are part of a certain niche.