Before you plug that flash drive in...
Here are two good reasons not to use flash drives at the desk:
1) It could be damaged by improper removal (loss of $20-50)
2) Its use might be against department policy
As for the first reason, our computers are not set up to allow us to safely remove hardware from the computer, and the department staff have made a decision not to change the computers. So plug those flash drives in at your own risk!
Improperly removing flash drives is not a sure way of corrupting it; the danger only comes when the computer is currently using your flash drive (whether you know it or not). Most sources will recommend using safe removal techniques to protect your hardware. If you have all ready plugged your flash drive in, the safest way is to unplug it when the computer is off, but this should not become common practice.
As for the second reason, our primary concern at work should be work. While we are on the desk, personal tasks (e.g. reading) are generally permitted when they are light in nature, but as soon as they interfere with our ability to serve the library patron in the best way or our activities give our patrons the impression that we are not approachable, we should set these tasks aside. Tasks involving a flash drive will usually fall under the "too involved for work" category.
In my opinion, there can be uses of a flash drive that involve light tasks (e.g. reading from pdf files saved on your flash drive.) Nevertheless, each supervisor will judge for herself whether your task or use of a flash drive is appropriate.