There's so much confusion on this topic that I'm writing a treatise on the subject and publish it on my blog.
12026.1(a)(1) says you can have the gun unlocked in a car's trunk so long as the trunk itself is locked.
Also 12025 applies to concealed firearms, so if you carry your unloaded gun openly from your house to your car and then put it in the trunk you're ok.
If your car is parked on the street you can still do this, as long as you're not within 1000' of a school, in which case you pretty much need to have it locked in a case every time you take it off your property.