I use hitch racks 99% of the time, when I use my trunk rack it's a bit different and much less secure.
For the hitch rack, i'll loop a Kryptonite cable through it's self around the top or seat tube, then lock the other end with a larger than average padlock to the hitch on the car. The trunk mount I basically the same, unless there isn't a hitch. Then it get locked to the tow eye on the car. If there isn't one of those, it doesn't get locked or left alone.
But , any method of locking a bike on a car is simply to prevent the casual "hey, there's a bike unlocked" thief. A pad lock or cable can be easily cut with a big bolt cutter. I do it all the time at the shop, it's incredible how easy it is. Some cheaper thinner cables can be nibbled through with a regular cable cutter, doesn't take long at all. A Ulock will require a grinder, which takes less than a minute.
It matters more where you leave you car\bike and for how long than the type\method of lock you use.
I've never been worried about leaving my bikes for a lunch\pitstop on the NY Thruway. East New York would be a different matter all together.