Hello,
it seems ZOO is not processing standard Joomla content plugins, so rendering FlashCharts inside ZOO content will not work.
It is up on ZOO developers to allow processing all installed and properly registered + enabled Joomla content plugins withing articles and/or other content managed through ZOO extensions. If they do so - and it should be relativelly small update - then it should work as with standard Joomla articles.
Unfortunatelly, there is nothing how we could affect this within FusionCharts.