Usually how Apple works is that they like the ability to have proprietary cable connections added to their systems, such as Mini-DVI, Firewire, 30-pin iPod connection and so on. It's so they get more money with specific ports that go towards the devices they make (usually). Kinda like how Sony has Memory Stick Duo, which is just usually used for Sony products. Also, since Intel has not made it (USB 3.0) native on their systems, they probably have a say in what Apple can produce and in doing so, there is no USB 3.0. In turn, they agreed on something Intel made and put onto an Apple system. From what it looks like, Intel made Thunderbolt instead of trying to make the universal standard of USB 3.0 work natively on their systems.
But the only real reason for Thunderbolt is another monitor. Why not just use Mini-DVI or just a normal DisplayPort?
That is what I take from it anyways.