John Traver writes about Happy Feet:

"the movie can in fact be read as anti-Presbyterian and crypto-Catholic."

Becky and I had a similar take.  Except, we didn't think the Latinos were Catholic.  Their worship centered around the charismatic authority of their combination shamanistic pagan witch-doctor Black Baptist preacher.  The movie contrasted the two religious cultures, but also showed both religions to be false, however important for maintaining a set of shared values.  The Presbyterians couldn't see the common grace in dancing, but learned to dance when threatened by the aliens when they proved to be real.  The Latinos valued their charismatic leader, but in the end he was a powerless liar, a showman, who tragically misunderstood or at least miscommunicated the nature of his necklace.  Perhaps it's my Scottish background, but the movie delighted in the fun of song and dance at the expense of true and false religion alike.