Once again I've put on the DFU USB bootloader onto the AVR AT90USB1287, after reading the bootloader PDF without any disctractions :D There I read that the chips need a full erase before you can program them over DFU. Did that. Than I also found out that I have to start the program I've burned ... oh well :) works! Awesome :) - now the actual programming can start :D

# If nothing works, try it with the force :D
sudo dfu-programmer at90usb1287 erase --force

# "Hexe" means witch, this is not witchcraft
sudo dfu-programmer at90usb1287 flash main.hex

# the bootreset fuse starts the bootloader after the reset
# so you won't start your program but restart the bootloader 
sudo dfu-programmer launch --no-reset