Ok I've solved it.
It was my fault, the -r parameter must have a list of Qt Resource files..
I got a bit confused with the fonts/ path, I though it was a folder but it's a prefix path a Qt Resource file (.qrc):
<RCC>
<qresource prefix="/fonts">
<file>MyFont.TTF</file>
</qresource>
</RCC>
and the command:
binarycreator -c config\config.xml -p packages -r resources/rc.qrc MyAppSetup.exe