Where the iMac, MacBook Pro and Mac mini sport Intel 'Light Ridge' Thunderbolt chips capable of handling four 10Gbps channels and two displays, the 'Eagle Ridge' chip used in the Air only makes provision for two 10Gbps channels and one display. (The Thunderbolt technology was codenamed 'Light Peak'.)
No big deal. While I do know one or two people that connect dual external monitors to their notebooks, they are a small minority. One (or none at all) is far more common. And the graphics controller in the Air can only handle one screen anyway.
You're unlikely to need the full 4x10Gbps capacity anyway, and the per-channel performance is the same with either chip. The Eagle Ridge chip used in the Air is physically smaller, making it a sensible choice when designing a notebook. Mind you, the Mac mini is a compact device too - presumably Apple considers its use as a server calls for the full I/O capacity of the Light Ridge chip.
If you've got the dosh, plugging a MacBook Air into Apple's Thunderbolt display is a nifty way to work when confined to a desk. Apart from a 27in screen, you also get three USB ports, a FireWire 800 port, a Thunderbolt daisy-chain port, speakers an a video camera - all available over a single Thunderbolt connection. And there's a built-in MagSafe charger.