So I noticed this just today when I was watching some jet aircraft fly around and stuff.
When the engine is at idle, or getting ready for takeoff the nozzle is supposed to wide open. When the engine is at full power (without afterburner) the nozzle is supposed to be small, and when the afterburner is on the nozzle opens up again.
In SimpleRockets 2 the engine starts with the nozzles in a small setting, and increases to large when the afterburner is on.
Here is what the SR2 nozzles look like: SR2 Nozzles Video
Here are two videos showing what the nozzles should be doing:
That bothered me too. Did no one else watch Top Gun a billion times?