Just an update on my first reply.
First of all, thanks A LOT aRock10, you almost solved my fan issue.
I bought BookArc too, and I can confirm the fan noise stopped. BookArc is just an example, probably every stand that avoids contact of MBA with the desk will work.
CPU temp is still quite high when watching flash videos,etc , but overall temp is fine.
I didn't like the idea to simply ventilate more my MBA, in my mind this is not a real fix: I think if one product (MBA) is publicized in bundle with another (Thunderbolt Display) the setup MUST work. I'm very disappointed that Apple simply ignores this issue, this is not the way to handle the problem.
Apple claims MBA and TD are fully compatible, one of the main features of new MBA with thunderbolt port is new displays support.
I mean, here with a description and a huge image of MBA and TD working togheter
http://www.apple.com/macbookair/features.html#thunderbolt
here with another huge image of both
http://www.apple.com/displays/
and in apple stores, where Apple guys confirm you can use them together without any problem.
This is not true and even if someone is lucky enough and has a very cold desk or office, Apple should help and find a fix or official workaround.
Fans start in unpredictable way: you can have 30 apps running without problems, but open a single flash streaming video, skype video call, etc when connected to TD and your fans will start spinning at 6500RPM
I don't care if this is not a SW fixable issue, Apple should address it as they did with antenna problems on iPhone4 and f.e. they should give a stand for free with any MBA and TD sold together or at least they should say on KB this is a known issue and they are working on it.