The film asks: What creates a better lasting society: science/technology or Christianity?
Both Allie (Ford) and the missionary, Spellgood, take their families to the Mosquito Coast to start societies. Allie's society fails because of his devolving megalomania, whereas Spellgood's is obviously successful -- his village is clean, orderly and happy; they have built a magnificent facility and comfortable housing; his people are clothed and fed; they sing so sweetly that Allie's children mistake them for angels. Spellgood's people may have given up some freedom but in return they had a thriving, disciplined society. Spellgood's success naturally gives birth to another evil within Allie's heart: envy. He becomes so envious & hateful that he literally tries to incinerate Spellgood's jungle utopia!
Of course, Spellgood isn't depicted as the 'good guy.' It's obvious that he's a bit of a loon himself with the typical negative connotations of Christian ministers usually seen in movies. In fact, it's clear that Spellgood is a megalomaniac like Allie. So what's the difference between the two? Unlike Allie, Spellgood has faith in -- and submits to -- something beyond himself, something greater -- God -- and this belief and reverence keeps his pride in check; it keeps him humble. Evidence of this is shown in the church scene where the congregation watches Spellgood on TV; his sermon doesn't attempt to bring glory to himself but rather focuses on teaching the people how to commune with the Almighty, using a telephone as a simple object lesson. Which brings us to...
Having no faith except in yourself is not good. Allie believed that technology and his genius alone would save them, but it was this that destroyed them. Allie had no faith but in himself. When this happens one's pride remains unchecked and will run its natural course. Most important to him was freedom -- yet only [b]for himself[/i] since he was a tyrant with his family.