I talked to a shooting buddy of mine who lives in Illinois. He said the laws are as follows: The gun must be in a container (safe, case...) designed for a firearm. The gun can not be loaded, meaning no rounds in the chamber and no loaded magazine in the gun. Ammunition and loaded magazines can be in the case with the gun (i always keep them seperate just incase I run into a A-hole cop). The gun and case must not be within reach of anyone in the car, so the best way to do it is put the case in the trunk. The case does not need to be locking, but I always have mine locked in the trunk when im driving through Illinois.
My buddy did say that if driving through chicago and a cop finds the firearm it will not matter how you store the pistol you'll be arrested. Cops in chicago get bonuses for making weapons arrests.
Dont take this as any legal advice, make sure you check out all the B.S. laws Illinois has before you go.