In my case, a big part of it comes from the observation that anything can be made popular with judicious application of sacks of money. Consider Yu-Gi-Oh. So, naturally, I'm always suspicious of anything popular. Most of the time, it tells more about the talent of a nameless marketing manager in a nondescript office tower in Tokyo or New York, than about the show. Not in Naruto's case.
So, Naruto is great. One indication is that I went through 125 episodes and it's still as fresh as ever. It's probably the longest series I have watched, ever. I thought about analyzing why it's so good, but I don't think I have good answers.