I have faced this situation many many times.When i have to use my pen drive,which is already containing some important data that i can't afford to loose, on a shared computer system that is probably infected with viruses, i always found myself in a dilemma.If i use my USB drive on that virus infected computer system then that virus will be automatically transmitted to my pen drive also and then it might make my pen drive unreadable or data on pen drive might be lost etc. depending upon the virus activity.But now i have found a solution for this situation.If i make my USB drive non writable then any kind of data can't be written to it,means if virus infected computer is going to transmit any virus to pen drive then it can't be written to it as USB drive is write protected.
Now your pen drive is protected on that shared system but i still recommend you to use a quality anitvirus software updated regularly as your system contains more important data than a pen drive.