As noted by AnandTech, Apple is using smaller and cheaper Thunderbolt controllers in the new MacBook Airs released on July 20th alongside new Mac Minis, OS X Lion, and the Thunderbolt Cinema Display. The website notes, whereas the 2011 MacBook Pros, iMacs and Mac Minis use Thunderbolt controllers codenamed "Light Ridge" with four bi-directional channels at 10 Gbps (thus achieving 80 Gbps aggregate bandwidth), the smaller chip implemented in the MacBook Air, called Eagle Ridge, is a scaled-down version with access to two channels. Furthermore, whilst Light Ridge comes with up to two DisplayPort outputs, the MacBook Air's Thunderbolt controller has only one DisplayPort output.
Eagle Ridge is available in two form factors (normal and SFF) and is effectively half of a Light Ridge chip. That means you only get two Thunderbolt channels and one DP output.
Presumably to cut down costs, save motherboard space and have a better impact on battery life, Apple decided to use a smaller version of the Thunderbolt controller that made its first appearance in February on the new MacBook Pros, first to feature the Thunderbolt technology co-developed by Apple and Intel and originally named Light Peak. It was previously reported high production costs of Thunderbolt ports could be the reason behind relatively slow adoption by third-party accessory makers. Currently only a series of high-end RAID configurations are available on the Apple online store and Apple's own Thunderbolt Display is set to ship sometime next month. You can read more about Thunderbolt here.