Yes, Kakashi is a jounin, and yes Naruto didn't make it in the chuunin exam. But you have to remember that these ninja ranks aren't based on power or strength, but on discipline, tactical skill, and most importantly: taking the exams.
After the chuunin exams in the beginning of the story, Naruto leaves the village and was never able to take another exam. After he grows up and comes back to the village, everybody (his schoolmates) is a chuunin and Neji is already a jounin. He just didn't take the exams. I'm pretty sure he was disciplined and trained enough to make it to jounin.
Kakashi might be a genius tactician and skilled in everything ninjutsu, genjutsu and taijutsu BUT he has the chakra content of a small puppy, as seen here, so in the general rank of power, he can't make it very far.
But that's about it, actually. His lack of chakra is his great downfall.
I would actually argue that Naruto surpassed Kakashi right about the beginning of Shippuden. Now, Naruto didn't have control over kyuubi then yet, nor did he have sage mode then BUT STILL, if he could dodge few raikiris (I remember this number being three, but couldn't find sources) that Kakashi is able to produce, he could beat him. At that time, it would be the battle of Naruto's life, but two chakra tails from Kyuubi would probably be able to handle that. If you think that that's too early, go forward a few episodes (40 to 43) and you have Naruto almost killing Orochimaru, that is reportedly stronger than Kakashi.