The Knights of Templar
This cult's inclusion in the novel is not exactly clear. The symbolic discussion becomes more clear if one understands the mythology associated with this brotherhood. The question of the cult is really the question of a powerful esoteric cult with secret knowledge with which they run the world. Is there such a secret society or not? The question is an attempt to solve the paranoia that Casaubon feels about the world. It feels to him like someone is secretly running the show, controlling the daily comings and goings of political and economic change.
The mysticism of Brazil
When he departs to Brazil, that is a hero's journey into a part of himself that wasn't available to Casaubon in Italy. He separates himself from Italian culture and politics for long enough to journey into himself. This journey takes him on a mystic path; he meets an important native named Amparo who symbolizes blended states of being because of Amparo's mixed ethnicity, and he journeys even deeper into the witchcraft of Bahia. When they venture too far into the mystic trances of Brazil, Amparo and Casaubon have a fight and she leaves him. He ends his journey and returns to Italy, newly informed by the cyclic journey into Brazil's underworld.
Alchemy and witchcraft
The journey coincides with Belbo's rise to esoteric alchemical knowledge. Now, they combine their knowledge and profit by publishing books about metallurgy (the alchemical process of transmutation metals into more valuable metals), but this is a symbol for their own souls. They aren't just transforming metals; they are transforming their own experience into a new, more valuable form which they can then sell in the form of books. The symbol is related to language as a magic power.
Language as a political statement
Language allows Belbo and Casaubon to transform their personal revelation into interesting literature, and even before that, their attachment to language is highly symbolic. Casaubon decides that his attachment to Philology is a political statement (Philology is the field that preceded Chomsky's school of Linguistics, which also included a heavier focus on mythology and literature). The political statement is independence of thought, and so he is concluding symbolically that to understand words and language is to free one's self from the party lines of widespread political opinion. In short, he is a heretic because he is perfectly independent.
Orthodoxy and mysticism
The question of political uncouthness becomes something else by the end of the book. The occult question of their research is partnered with political sentiments that verge on radicalism. Together, these form a motif about the characters. The characters are political heretics. In the same way that witchcraft was condemned by the church throughout human history (often including mysticism, Gnosticism, and alchemy, which are all discussed in the novel), so also, Casaubon and Belbo are heretics to Italian politics because they know too much to believe the insipid narratives that dominate political discussion.
