esptool.py is your friend. Simply do:

./esptool.py --port /dev/ttyUSB0 write_flash 0x00000 ~/Downloads/nodemcu_float_0.9.6-dev_20150704.bin 

This works for my esp-01 module. However for the NodeMCU v2 module that I have, more options need to be add to the command line:

./esptool.py --port /dev/ttyUSB0 write_flash 0x00000 ~/Downloads/nodemcu_float_0.9.6-dev_20150704.bin -fs 32m -fm dio -ff 40m

It probably has to do with the larger flash size for the v2 module. However, I don't understand why it would not work with the old command.