Flex is probably better than CF for charting if you don't mind requiring Flash. Flex is just a framework for Flash, so technically you could do it all in Flash, but it would require 80,000 more lines of code (rough, exaggerated estimate).
CF Charts has options for Flash or Image charts. Image charts don't require flash, but also can't be interactive.
If it were me, I would use neither. I would use one of the incredible JS charting frameworks that are now available. For my projects I use HighCharts. http://www.highcharts.com/
It depends on your requirements. The cfchart format = jpeg is handy because it's easy to copy the chart into emails, powerpoint presentations, etc.
Thanks for the suggestions.
So how does Flex fit into this?