I will be interested to see the replies to this. It is a topic that frustrates me a lot that this is relatively difficult to do......
The only solution I have found is to modify the 'launch' html document, and use the external API from flex to have the launch document display the PDF.
Flash player do not have the necessary libraries to display PDF. But AIR runtime does ( http://livedocs.adobe.com/flex/3/html/help.html?content=PDF_1.html ).
Not a good solution, but somehow you need to convert the PDF to an SWF to be able to load it into a Flex panel.
Iframe trick ( http://code.google.com/p/flex-iframe/ ) can also be applied here.