Apologies for the trouble. We tried to pick an extension that was not widely used, but as noted, it's virtaally impossible to choose one that isn't used at all. (And no, this issue did not come up during beta testing.)
In any case, file type associations are ultimately in the user's control. Under Folder Options > File Types, you can re-associate .air with Flight Simulator. Also, for any given .air file, you should be able to select between relevant applications by right-clicking and selecting Open With.
Hope that helps, Oliver Goldman | Adobe AIR Engineering