Not exactly.
There is a license in the sense that manufacturers must sign a license to use the parts, committing to approved designs, and gaining certification before being sold to customers. The ecosystem requires all devices to be certified.
Hi-speed design does entail higher development costs due to materials and test equipment required for validation. There are also certification costs.
There is also complexity. In addition to the Thunderbolt controller chip, there is quite a bit more going on inside than a simple USB-to-SATA bridge. Take a look at some of the reviews and teardowns showing the insides. USB-to-SATA controllers are simple in comparison. I don't think Thunderbolt will ever be reduced to as simple a solution, though the complexity is being reduced.
Overall system cost is higher due to circuitry, cabling, DisplayPort, power management, and overall bandwidth.
Yes, the controller is sole-sourced from Intel, and yes the controller is more expensive than a USB-to-SATA bridge chip, but not $100 more.
Close examination of the Apple Ethernet and FireWire dongles do indicate reduced complexity as there is no daisy-chain capability, so simple bus-powered devices could be less expensive but still ore costly than USB.