Assuming an iPhone can play wave files, there should be no conversion involved. The device might have some EQ (I'm not an iAnything user so I don't know) so you'll want to verify that if there is, it's set to Flat.
A more likely explanation is that it's not the iPhone's fault, but rather the limitations of your car's sound system causing the mix to not translate well. That's the real challenge in this business: making mixes that sound acceptable no matter what you play them on.
It's not easy! I would caution you, however, against tailoring your mix for the car, as that is a losing proposition that will just have you chasing your tail. A car is an acoustically-challenged environment, with lots of reflections and resonances. Think about how automotive engineers literally design car doors to be drums, so that they make a satisfying thump when you close them. Those doors are resonant cavities! And where are your speakers mounted? In the doors. And if you have tweeters in the dashboard, look at how their aimed: in most cars they're aimed at the frickin' windshield! Can you say "comb filtering"?
On top of that, most car stereos have a built-in bass boost to disguise the fact that you can't get good bass response in such a small space. They typically have an artificial bump somewhere around 60-100Hz. Consumers generally don't care if it's flat, they just want to feel the bass. But it sucks as an EQ reference.
Which is not to say it's a waste of time to check mixes in the car. For me, it's the ultimate test. If it sounds OK in the car I know I've got a good translatable mix. What I
don't do, though, is alter the mix specifically for the car. It will never sound as good in your car as it does in your studio, and if you do manage to get a great EQ in the car it will probably sound bad everywhere else.