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As long as you wipe and format the flash drive from the secure computer every time you use it, there shouldn't be any risk. I don't think even Stuxnet could have infected a linux machine that didn't mount or autorun the partition.

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Flash drives are not dumb. I know that Travis Goodspeed has had some success in reflashing their microcontrollers to speak corrupt USB to attack USB stacks of host machines (which of course run in kernel mode).

I guess the only safe options are CDRs and one-way ethernet connections.

A fascinating talk by Travis Goodspeed on the mayhem possible by reprogramming the USB controller in a disk:

http://www.youtube.com/watch?v=D8Im0_KUEf8

Writing a Thumbdrive from Scratch: Prototyping Active Disk Anti-Forensics

Stuxnet was bespoke malware with multiple 0days--the reason it worked like it did was because of how the target's computers were set up. If Iran had used Linux they would have likely used different vulnerabilities to [try and] accomplish the same goal.

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