Neji, sasuke, and itachi were hereditary. rock wass the genius of hard work. so was kakashi, minato, negato, orocchimaru were also such geniuses. but what of naruto?
out of stubborness and experience. after a while he learned that running into a situation wasn't always the best and then thinks about how many times he's been injured and decides to plan =)
If you want to get technical then technically Naruto isn't a genius. It's part of the separate between Sasuke and Naruto. Sasuke is a genius with natural talent who learns things easily, and Naruto is the hard-working type who doesn't learn things easily and pushes himself through rigorous training.
i think.... he's really a genius... it's just that he chose to be stupid at the beginning for the people of konoha to recognize him.... they recognize him as a stupid brat.. but as he goes on... they realize he's not all that... he's a genius who follows his heart... and the bravery to stand by his words... xd