It likely uses a different display technology, has thicker glass and a thicker frame to boost rigidity, and then there's the ports too, and probably a thousand other things I don't know about as well.
Take a look at the teardowns, there's more circuitry in the thunderbolt display than the iPad Air which is interesting.
http://www.ifixit.com/Teardown/Apple+Thunderbolt+Display+Teardown/6525
http://www.ifixit.com/Teardown/iPad+Air+Teardown/18907
With so much available space, they could have added a gpu. That would be a great addition to Mac mini and MacBook owners.