The reason people who don't like Napoleon Dynamite don't like it is because subtlety has been destroyed for them entirely by a movie industry hell bent on feeding people a crack-cocaine form of filmmaking/product... they can't get "high" on anything subtle, they've burnt out their receptors for the subtle and sublime.
ND is the essence, if not a new manual, on subtle. Even though throughout the film one could argue that its rudaments are too exaggerated and blatant, that doesn't mean it wasn't subtle. ND had a collision of three factors at once -- lost culture, stagnant culture and no culture. Napoleon himself is like a life-seed of change (heck yes!) into a vaccuous Idaho hellhole of mediocrity and sameness. A lot of people thought this movie was set in the 80s. It's not. The opening DVD titles show Napoleons own school ID for the year 2004-5. Uncle Rico is "stuck" living in '82, psychologically. In fact, the whole town is stuck in the 80s. Napoleon represents the "Angus" (another good film) factor, the deformity in the midst of conformity that, if it fight back and refuses to be absorbed, can actually cause a super-culture to arise. All your wildest dreams will come true... if you vote for Pedro. Which is a vote for Napoleon, a vote for change, a vote for destroying mediocrity from within, by a germ process... however weak and unformed as it may be. However subtle it may be. Once Napoleon invokes the total black funk boogie dance into the bloodstream of this High School rotting away under the effects of "sameness" and status quo, the universe turns upside down and the wildest dreams come true (notice the difference in Deb's appearance at and post-dance). Pedro becomes president, and his eyes tell us his aspirations don't stop there. Uncle Rico gets is girl back. Tina finally gets fed by someone who loves her. Napoleon catches a delicious bass for Deb. Kip merges with LaFawnduh shattering all potential barriers.
I think ND is a lot deeper than people give it credit. People who don't want or like deep won't care anyway, both those who enjoy the analysis of film will see it, even if they aren't particularly enamoured with it as a movie. It's not a "great comedy," its not intended to be.
I doubt if the makers ever imagined people would be laughing to the point of tears over simple phrases like "Luckyyyyyy!" or "Eat your FOOD!" People are reacting to the tone in Napoleons voice more than what he's saying. That tone is something they can resonate with -- dissatisfaction.
Napoleon is utterly, tragically, painfully bored with everyday mundanity, and so are we. His sighs and moans of pain are quite real, and it's what we'd all do if we were as emotionally sound as Napoleon. I argue that ND is a superhero fantasy, where the super hero comes from out of nowhere to revolutionize life for himself and everyone else, with just a few simple modifications to the existing system. Just enough to where some of the happiness being horded by the status quo robots of the system gets more evenly spread around.
I think by and large the people that hate this movie are people who don't realize that what was missing in ND is what they've been spoonfed in every "alternative" film for the past 20 years and are now addicted to, and that's melancholy, defaming of a deity or corruption of innocence or purity, strings of profanity (profanity has its place, of course -- Glenn Gary Glenn Ross/ex), things exploding in 200 foot balls of fire, sick undercurrents of despair without resolution, maniacal vengence and maybe most of all, simple humanity.
There's a scene that sums it all up. Deb, Pedro and Napoleon are standing looking at the dance floor. They form a wall in pale blue light, totally still, against the contrast of the warm reds and yellows and movement of the people dancing. They are utterly cut off, in the darkness, though allowed, permissively, to participate. But they don't really belong there and they know it. And all that is about to change, with Napoleon Dynamite. He is dynamite that is set to go off and knock that wall down, and bring dynamic change.
ND is a masterpiece of filmmaking.
*PS: if you have a home theatre system for good sound, the DVD has excellent sound digitization. The musical parts just rip right out and your subwoofer will bounce like crazy, and yet, not at the expense of normal vocal sections like many DVD dolby implications. VERY impressive effect.
VOTE FOR PEDRO!