How do car dealerships make any money?

I went to the car dealer this morning, expecting to have the guy look at my car for five minutes. I left the dealership about two and a half hours later. In that time, all that happened was a guy looked at my car and then told me I couldn’t have the options I wanted. All I wanted was a car with a dark interior and a navigation system. Navigation systems are hard to come by, and so are specific colors. Well, I got the color I initially wanted anyway (silver), and it looks like the cars with the dark seats still have beige-y plastic so they look a bit silly. I paid a non-refundable $500 deposit and they’re going to call me in a few weeks when the car comes in. I’m hoping “few” means a couple of weeks and not a lot more.