I'm not sure the definition of "hub" is engraved in stone anywhere, but the sort of cheap USB hubs you're talking about simply share the bandwidth of one port between multiple devices. That's fine for (say) connecting a mouse, keyboard and other low bandwidth devices, but connect two disc drives to a hub and try and copy between them and things will start to crawl.
Thunderbolt hubs add new controllers, with their own bandwidth. They also add interfaces that don't exist or aren't externally accessible on the host computer (like eSATA, USB3 and, if you have an Air, FireWire). Yes, you could get a similar effect, a lot cheaper, by buying a PCIe multi-io card, but good luck plugging that into a laptop with no PCIe slots.