click on file/publish settings/formats.
is there an mov format? if yes, you're good to go.
I wish it was that easy. When I choose to publish in MOV, I get the message: The installed version of QuickTime does not have a handler for this type of Macromedia Flash Movie.
assuming you have an up-to-date version of quicktime, that looks like a quicktime issue: the "newer" mov format may be different from the "older" mov format.