Presumably the flash drive is being used to transmit data to and from another (less secure system). If you use a new (known safe) flash drive every time and only transmit data out of the secure system you should be okay.
Anything else has vulnerabilities, even to script kiddies. Imagine the second computer is seething with viruses, and it contaminates the flash drive as soon as you insert it. Try to format it on the virus-laden computer and it loads it with the virus at the same time. Stick it in the secure computer to format it and it infects the secure computer.
That sure helps.