Criticism of Europeans
When Joabin explains Bensalem's superb moral character to the narrator, he does so by comparing the "chaste" people of Bensalem to the otherwise corrupted people of Europe, where the narrator is from. Of course, readers of the text at the time would have also been Europeans, and Bacon's text nods ironically to the fact that European society was imperfect and lacking progress.
Church and State
New Atlantis celebrates, not the separation of church and state, but their union. Their union, however, is devoted to ongoing scientific practice rather than to integrating Christianity into a justice system. Thus, Bacon's utopia reflects a form of government that looked a lot like the one Charles I (the monarch at the time) was touting – that based on the divine right of kings. However, in actuality, Bacon replaces the primacy of the monarch (the state) and the primacy of God (the church) with the primacy of science and scientific inquiry.
Merchants of Light
Though this term is never used in the text itself, Bensalem is portrayed as a utopia – that is, an ideal and perfect society that nobody would presumably ever want to leave. Indeed, the Governor of the House of Strangers explains that few foreigners have ever come to the island and returned home, electing instead to stay and be provided for by the state. It is ironic, however, that in order to maintain this utopian vision, Salomon's House must still remain connected with the rest of the world by sending the Merchants of Light out every 12 years to gain information about progress, exploration, and discovery. This phenomenon becomes part of the utopian vision, suggesting that a true utopia would not detach itself from other civilizations entirely.
Unfinished Text
In many ways, it is ironic that a text purporting to describe an ideal and utopian society would be left unfinished. New Atlantis only scratches the surface of how a utopian nation would be structured, and though it provides detailed explanations of Salomon's House through the conversation between the narrator and the father, the incomplete text leaves much to the reader's imagination.