I wanted to use Cairngen in a recent project and quickly noticed that the standalone version of Flex Builder 3 does not have Ant support available by default. Getting it set-up is pretty easy though:
When Flex Builder starts up again, you will have Ant support available (e.g. any build.xml files will have a little ant on the icon). You can also verify by selecting Window -> Other Views... and checked if an Ant directory exists.