Well, it's actually because Thunderbolt requires an Intel chipset. Apple helped develop Thunderbolt, but Intel owns the tech, and it is only supported by certain Intel Core-series chipsets. The ARM architecture does not support it, so Apple cannot include it without using Intel processors and their supporting architecture, something that Intel hasn't figured out how to get into a power-conscious, super-mobile form.
Thunderbolt is a combination of PCI Express and Displayport, using Apple's Mini Displayport connector. So, the chipset is too big to fit, Apple wouldn't use it if it could (not as efficient as ARM), and the connector is actually
thicker than the 30-pin dock connector.
Believe me, Apple would have included it had they been able to, but it isn't there yet.
