Okay. I got this one.
-kun and -san are both honorifics and you seem to know how to use them. However, they have very different connotations to them.
"-kun" is for someone you are familiar with, like a friend; you are older than them; or higher up in status than they are. This honorific is used only for a boy, though. The girl equivalent is "-chan." So whoever is calling Naruto "Naruto-kun" is most likely a friend.
"-san" is the English equivalent of "Mr.", "Mrs.", or "Ms.". Whoever is saying this probably does not know Naruto very well. Or they are just showing respect because they are younger.
I think that covers it, but if I need to clear things up, feel free to ask.