I found a solution but I'm not totally satisfied by it.
First, you have to make sure you checked Flex font manager when installing the Flex and AIR SDK.
The last version of Apache Flex seems to have a problem with embedding CFF fonts. Since the embedding worked fine with an older version (Flex 4.10 AIR 3.8), I copied the jars in /lib/external/optional.
afe.jar was the only one with a significant size change (1.37Mo -> 626Ko). It must be the one used (CFFFontManager is prioritary but doesn't work...) because now my fonts are displayed. There is an ugly padding though.
If someone finds a solution that allows to use the expected CFFFontManager, it'd be great.