Many mp3 drives can connect to the car stereo via the usb port - so an aux port isn't needed.
To me, the benefit of an mp3 player over a thumb drive is that when you get to your destination, you can connect the included earphones to it and continue listening. With the thumb drive, you have to have another device to continue listening.
In the end, there are many solutions - all have their pros and cons. It's up to the individual to decide which is best for them. It's not a "this is the only way to do it".