I wanted to move some Prop2 software development to my main workstation, which runs Ubuntu 12.04 64bit (the "Long Term Support" version)
PNut appeared to run fine under Wine, but it could not find the PropPlug, which was at /dev/ttyUSB0
The (easy) answer was to map /dev/ttyUSB0 to COM1 for Wine, which you can do from a terminal by executing the following line:
ln -s /dev/ttyUSB0 ~/.wine/dosdevices/com1
For a nice simple terminal program just use GtkTerm, which you can install from the Ubuntu software center. Just remember to close it before programming the P2 emulator.
Your PropPlug may show up on a different /dev/ttyUSBn