What version of the SAMD boards package are you using? I have 1.6.2 installed and there is no cpu menu. It looks like you meant to specify f_cpu but there is no menu for that either. The parameters part of the --board option should only be used to specify the desired selection when there is a custom Tools menu for the selected board. So try:
arduino --board arduino:samd:arduino_zero_native --port COM11 --upload "C:\Users\Itay Dagan\Documents\Arduino\Blink\Blink.ino"
itayd100:
Do you also know how to upload a sketch without compiling?
I'm not very familiar with the Zero but what I'd do is turn on verbose output during upload in File > Preferences and then upload a sketch in the IDE. Then you should be able to just copy the command that is used for the upload. This works fine for me with avrdude commands for AVR boards so it should be the same for Zero. It won't be done by the arduino.exe command line but rather the tool that is used for uploading to the Zero.