Yes, it will work fine. The only real difference is that the Futaba plugs have a little "tab" on the side. Kind of like a guide so that you can only insert the plug one way (the correct way). You can use the Futaba plug in just about all other systems as well, just simply shave off the little tab.
Most plugs now days are interchangeable. The only exception I can think of would be the Traxxas servos. Their plug is consderably larger than everyone elses. So to use it on another system, you really have to some serious shaving. Also, look out for the old style Airtronics servos. Their wiring pattern is different.