The love ceremony
Mary invites the supernatural elements of the earth into her journey toward love. She does this by invoking the spirits of love in a rite performed in the forest. The ritual is rewarded, but not in the way she wants. This is an interesting symbol, because it shows a nuanced aspect of her European sensibilities. She is willing to get freaky with her religion because she is lonely, but when the universe answers her in a way she doesn't want, she denies it and just does what she originally wanted anyway.
Hobomok and Charles Brown
The tension between the answer given by the forest (Hobomok) and the answer Mary wanted (Charles Brown) is a symbolic tension, because it shows something elemental about her role as a woman in the selection of a mate. She is asked to choose between suitors, which leads to a kind of compare-and-contrast between the men and their communities. Hobomok is full of love, but he doesn't appeal to her cultural narrative. Hobomok struggles to see what she could possibly see in Charles that is worth more than his undying affection.
The symbolic hunt
When Mary attends a Native American hunt, she expects to see some wilderness in his spirit, but Hobomok shows his true colors in a different way. He is meek and kind, and he doesn't really have the heart to kill another animal. This symbolizes an aspect of Native life that Mary was unaccustomed to—not only is Hobomok "primal," he is also deeply spiritual and perhaps even enlightened. His love is tender and universal, and she struggles to make sense of it.
The London Company conflict
The conflict between the English and the Native Americans is most clearly symbolized in the London Company conflict that Hobomok tries to quell. He talks to both sides, trying to share with them what he knows from his love for Mary—that they are all essentially the same, and that fighting only leads to more fighting. Nevertheless, they ignore him and maintain their conflict. He cannot enfranchise a peaceful point of view because they have believed cultural narratives about "the other" that cannot be changed through reason.
The wrong marriage
The novel doesn't end with Mary finding some deep desire for Hobomok. She has already made her mind up about the worth of a Native American. Her decision to marry Charles is symbolic evidence that even Mary, with all her exposure to Hobomok, could not find true empathy for him as a human being. Surely, Hobomok's love was the answer to her pagan ritual, but she ignores the elemental forces and marries an English man, to Hobomok's chagrin.
