It's largely because of context. I *hate* how my dealership inserts itself between me an my purchase and tries to siphon off money for itself. I went through the trouble of looking for the *same* model and make of my previous purchase between two dealers - and got two "rock bottom" prices that were $1000 different. I know they were "rock bottom" prices, because the dealership told me so.
Now, it depends on the total price of the car but, given a new car in the $30k range, that isn't a big difference (Would you be upset if someone said a rock bottom price was $100 and another said it was $97?)
One dealer may be paying a lot more to occupy their lot - or may have less sales volume, requiring them to make up the overhead over fewer purchases.
Now, I'm not saying you want to pay $1k more but, percentage-wise (assuming a $30k vehicle) a 3% difference is pretty minor - or may be due to something as weird as different rims on the car.