Flex code can be used with any version control system I am aware of.
I was unaware that Flex Builder had native support for any version control.
However, Eclipse, which Flex Builder is based on, has plug-ins for a lot of things, including version control systems.
Take a look at the team development category here: http://www.eclipseplugincentral.com/
Version control can be a very big problem, if you truly want to make it work. Backing up some source files on a disk may be all you need. But if you want a workgroup to restore old versions over time, you've got a lot of planning to do.
I'm pretty sure there are Flex Builder / Eclipse plugins for Git, but what's wrong w/ the command line?