Hobomok knows something profound through his affections that his community is blind to in their rage. There is nothing in his life that would dissuade him from being with Mary if the opportunity presented itself, but his culture strictly prohibits it. The fact that Mary doesn't feel the same way about him doesn't cause him to abandon love, either. He knows through just the feeling he experiences about her that he could love her, and that is enough to convince him that the warfare between the two cultures is set on false pretenses.
The Europeans have beliefs about the Naumkeak natives that are established on false pretenses that are explored in the London Company conflict, where Hobomok tries to talk sense into people who simply will not listen. Nothing he says can help quell the conflict, indicating that the real problem here is a kind of unwillingness to consider the humanity of the other side. Hobomok knows more about this dynamic from his own culture, but he sees through the prejudices because he is in love.
The love is natural and perhaps even supernatural, Hobomok feels. Its natural aspect shows him that he and Mary are of one kind. Their costume and culture don't change how he feels about her, nor does their cultural history of conflict and violence. However, Mary doesn't see this. Even when she prays to the spirits for a true love (in the opening of the novel), there is nothing that can prove to her that Hobomok is a decent candidate. Hobomok feels he is her answered prayer, but she doesn't see him in the same way she sees Europeans.
Perhaps one way of deciphering this mismatch would be to say that the characters are symbolizing their respective communities. In that analysis, Hobomok would be more open to accepting Mary because his Native community might be more open to newcomers. However, Mary is convinced that Hobomok is less than her because he isn't European, and this prejudice is shared by her English companions. This single prejudice is enough to poison the waters between them.
