Naruto:
- Is an Uzumaki, so he has naturally large chakra reserves. Also related to Senju clan.
- Is the son of Minato, the 4th Hokage, who had a genius level intellect. To this day no one has posted higher scores in the academy than Minato, not Itachi, not Kakashi, not Shikimaru (who has a confirmed IQ of 200+), no one.
- Has the nine-tailed fox sealed inside of him, the strongest tailed beast aside from the ten tails. This boosts his already high chakra to obscenely high levels to the point he can make hundreds of clones as a preteen (remember, Shadow Clone Jutsu is an S class technique). Also gets free, gigantic boots to his physical stats if he taps into its power.
- Is a reincarnation of Asura. He is literally the reincarnation of the son of the Naruto universe's Jesus. Add another +boost to Chakra.
- Naruto was always going to be OP.
If anything, if you want to see the merits of pure hard work then its Might Guy. He nearly killed ten-tail Madara.
Went from a no talent loser to almost ending the war and almost killing the strongest being on the planet.
Naruto is a better protagonist than Goku though, I'll agree.