I would be the first to agree... Thunderbolt is technically better than USB3.
However, that is not the point.
What is the advantage of USB? Simple. The connector.
I can plug a USB1 device into any USB3 port and it works. The reverse it also true, albeit at a pretty slow transfer rate.
The point it, the USB plug is ubiquitous while thunderbolt is already planning to change the connector again. That means buying adapters.
That also means that the next motherboard I buy most likely wont have thunderbolt on it. Which means I would not be buying any thunderbolt devices.
My impression is that thunderbolt is marketed specifically toward "Apple" people. Since I am not an apple person, I cannot say if this next part is true or not, but the impression that non-apple folks have is that "Apple" people will replace their gadgets every year or two with what ever new thing Apple has come out with.
If that is true, the connector thing is no big deal since you would be starting over every time.