I honestly can't understand how you can "hear" the difference using $90 JBL speakers....in a car nonetheless. I mean cars have a LOT of noise just driving down the road in general, how could you possibly hear a little tiny bit of static caused by mp3 use?
It sounds to me more like you have cabling issues, more than you have a problem with the mp3's. Perhaps a better head unit, maybe even one with a direct iPod connection to it might be in your future?
You could also have bad signal wires going to the amp, might be too close to power lines, speaker wires could be picking up interference, there's TONS of things that can cause issues in car audio. Don't be blaming the mp3 just because you seem to be having some issues.
I honestly can't tell the difference in a car between mp3 and flac. I can tell the difference on my new home stereo though. And keep in mind, I had a $12,500 system in my car at one point....MUCH more high end than those $90 JBL's you bought