Children need a variety of life experiences to make them well-rounded. Confusion is one of those experiences. If everything that crosses your child's path makes perfect sense, then the cognitive dissonance they'll experience later in life might drive them to drug addiction or bizarre belief systems that don't stand up to rational analysis. And that is why you should take them to see this movie.
You should arrive late and avoid the new, unpleasant, mega-digital Sylvester and Tweety-Bird cartoon, the one where you can see Sylvester's suffering succotash saliva spewing right at your face. There's a reason that the latest Winnie the Pooh feature was in warm, hand-drawn 2D; some stuff just needs to be left alone.
Once the penguins take over you'll be treated to the spectacle of a million identical black-and-whites executing the choreography from Janet Jackson's "Rhythm Nation" video and singing a version of the song that's also mashed-up with "Sexyback" and LL Cool J's "Mama Said Knock You Out." So it's like any given moment of Glee, but with cartoon birds.
What happens next involves an "exquisite corpse" plot assembled from random doses of Robin Williams and eco-terror, subplots about krill exceptional-ism and Believing in Yourself, outcast babies and parenting failures, mean Australian elephant seals and dozens of other non sequiturs, all of it glued together with the over-arching non sequitur of singing, dancing penguins, with at least one of those sequences involving the inter-species transfer of air-guitar skills. If the successful re-release of The Lion King proved that it's a perennially effective animated sedative for kids then this franchise's ongoing popularity could well be its hallucinogenic counterpart.
There are moments of WTF excellence dotting the entire experience, stuff like hearing Matt Damon singing snippets of "Never Gonna Give You Up" and "Wake Me Up Before You Go Go" or watching a heroic puffin try to become a savior/cult-leader to all penguins just to get on their good side. And the movie's final act -- here comes a spoiler, but I think of it more as a selling point, so read on or avoid at your own discretion -- involves a baby penguin belting out a moving chunk of a Puccini opera before the entire cast, elephant seals included, get crazy with David Bowie and Queen's "Under Pressure." It's a surprising combo platter of weirdness, gloriousness and thumpingly over-the-top emotional pummeling. Don't ask how, just let it do its freaky nonsense job. You won't know what you just witnessed but you'll be oddly happy that you did.