I guess this is fairly obvious to most, but since I am a newb, and I could not find the answer by googling and instead found this by messing around, the way that I can connect to zedboard from ubuntu via the USB port is to open a terminal and run:
sudo screen /dev/serial/by-id/usb-2012_Cypress_Semiconductor_Cypress-USB2UART-Ver1.0G_821E81522717-if00 115200
If you use /dev/ttyACM0 you get zed-boot? Not sure what this is.