Scott Ridgeway's idea of keeping stuff in a cutesy diaper bag is a good one.
I've had to give some thought to bugout bags in my family's cars. I drive a boring little sedan, which means I can keep pretty much everything out of sight, but I have still made a point of keeping things that stay in the cars cheap and at least semi-disposable.
Other thoughts: just because YOU know it doesn't contain anything valuable doesn't mean that a would-be thief will know that whatever's in that backpack on the floorboards isn't valuable. So, even a backpack full of used textbooks may get your window broken by some crook who hopes it's full of treasures. A Bible in a Bible cover might look like a small laptop, and the fact that your prospective thief wouldn't break in to steal a Bible might not be enough to keep you from a broken window.
One thing I've done is to scatter gear, rather than keeping it in one bag. Rather than keeping pup tents in a bag, where they'd look potentially worth stealing, I usually just keep them folded up, with the poles tied together but otherwise in the open. While a bag might look like it's worth stealing, I doubt a couple of pieces of canvas and some wooden rods would. While there's a lot to be said for keeping one's gear in a single bag, for your mobility's sake, perhaps a good compromise might be to keep an empty backpack stowed away out of sight--say, with the spare tire, or under a seat--so that you can fill it up with the various essentials you've got scattered around the car in case you want to hoof it somewhere. Also can't hurt to have some redundancy--a couple of canteens here and there, maybe two or three cheap Mora knives tucked a little out of sight.
One more thing I have to consider is temperature variation. Anything in my car is going to have to withstand temperatures that will almost guaranteedly range between freezing and 170 degrees Fahrenheit (given that cars get a lot hotter than the outside air) over the course of a year. Thus, I try to keep things like leather to a minimum, and keep it well treated with oil, etc., to keep it from turning to powder; similarly, I keep Nalgene canteens in opaque pouches so that the sun passing through them can't get concentrated on the floor and start things smoldering.
You should make your BOB where you can take it with you and not leave it in the vehicle. Maybe you should puts some fiddlebacks in the bag. 
