I have a carry permit but I don't know the legality of having a loaded AR, even in the back seat.  Will I get cuffed and stuffed if I have a cased, loaded AR?

a CHP has no bearing since you want to carry a AR, i assume a rifle with 16" barrel.

it is an open carry state, except for a few exceptions.  (withholding LB68 rant)

but asking for legal advice on the internet is not too good.  if you really want to know, go ask a lawyer.  i recommend Dick Clark from Dick Clark Law.

Admittedly I don't roll around cities with it there, but I've had no issues. Maintain your vehicle, drive defensively, have a CCW and a rational reason to have a rifle in the front seat and you'll be fine.

What I was thinking was just throwing the case on the back seat but it has pockets with five loaded mags in it.

I understand about asking advice on the Internet but sometimes people have experiences to share and that's all I'm looking for. 

Legal to have a loaded rifle inside a vehicle, just not a shotgun.  Assuming of course like DHR said the barrel is 16" unless you have a stamp.

Yeah, both of mine are just your basic 16" carbines with optics.  My concern is getting pulled over for some reason and a cop dragging me out of the Jeep.  

I don't know, that's why I was asking how the law viewed it.

The law says you can open carry a rifle. Sure, at least in my jurisdiction. Officers also have a huge latitude in how they conduct a traffic stop. I've had exactly one TS in my time with a guy with an AR in the front seat, and worked the stop fairly normally. But he was local, and I knew of him, if not him directly. But depending on the area, time, your actions, attitude, etc might change how I view things.  Every officer and agency would treat it differently. I know just for me, it would definitely peak my interests and awareness.

Most likely scenario, if I wanted to do anything other than a verbal warning? I'd ask you to step out of the car, and conduct the traffic enforcement action from my front seat after ensuring you didn't have a concealed weapon on you also. Is it a stop for something other than traffic? Whole different ball game.