When Goodman Brown is in the forest and overhears voices that sound like the town deacon's and minister's, he hears the deacon's voice say,

Of the two, reverend Sir . . . I had rather miss an ordination-dinner than tonight's meeting. They tell me that some of our community are to be here from Falmouth and beyond, and others from Connecticut and Rhode Island; besides several of the Indian powows [sic], who, after their fashion, know almost as much deviltry as the best of us.

Thus, the deacon would much rather be present at the witches' meeting in the forest than be present for an ordination dinner for a new minister of his Christian faith. He is excited about the fact that so many new people are coming from faraway places to tonight's meeting. In addition, he mentions that there will be several high-ranking Indians religious men present who, in their own ways, know almost as much deviltry as the best of them, namely, the Puritans. In other words, then, the deacon seems to suggest that the Native Americans certainly know sin and wickedness, though not quite as much as the Puritans themselves (the very people who prided themselves on purifying the Anglican church and living especially sinless lives!). Despite the fact, then, that Goodman Brown seems to equate the Native Americans with the Devil, the deacon implies that the Puritans are actually more sinful and evil-natured than the Native Americans. This seems to turn the typical thinking, as embodied by Goodman Brown's ideas, about the native peoples on its head.

Further, when Goodman Brown actually gets to the witches' meeting, the narrator says,

Scattered, also, among their pale-faced enemies, were the Indian priests, or powows, who had often scared their native forest with more hideous incantations than any known to English witchcraft.

Thus, we have a very large crowd of seemingly pious Puritans with just a few Indians scattered among them. The make-up of the congregants, then, shows that there are more sinful Puritans than there are Indians. From both of these quotations, then, the Puritans end up looking more sinful than the native peoples.

There is a condescending attitude towards Indians (Native Americans) from Brown's perspective (not necessarily Hawthorne's). Brown expresses this just as he begins his journey of a "present evil purpose": 

"There may be a devilish Indian behind every tree," said Goodman Brown to himself; and he glanced fearfully behind him as he added, "What if the devil himself should be at my very elbow!" 

Here, Brown thinks that "devilish Indians" and the devil himself might be preying upon him. He conflates the two (devils and indians) implying that he thinks both are evil. 

When Brown sees his wife's pink ribbon caught on the branch of a tree, he loses his faith and maybe his mind. He takes on the personification of the devil "rushing onward with the instinct that guides mortal men to evil" amidst "the creaking of trees, the howling of wild beasts, and the yell of Indians." Again the ideas of evil, savagery and Indians are conflated. It would seem, here, that Indians are conflated with evil in general, not just from Brown's perspective. However, the paragraph ends with the narrator commenting that Goodman Brown "was himself the chief horror of the scene." 

Thus, Brown became the most frightening thing in the forest. As this story includes Hawthorne's criticism of the strictly religious and self-righteous Puritan belief system, it is a criticism of their condescending attitudes toward Indians. Puritans adhered to a strict Christianity and the most strict would look upon Indians as savages. Hawthorne knew this. Goodman Brown was such a strict and faithful Christian who, like those of his time, viewed Indians as savage and potentially evil. Since this is a criticism of those strict Puritanical beliefs, it is also a criticism of Brown himself. 

Although Hawthorne does not come out overtly in defense of Indians in the story, he does criticize characters/people (Brown) who refer to them as devils. So, within the story, the attitude towards Indians is condescending. Above the story and/or judging at Hawthorne's perspective, it is neutral to Indians if not sympathetic. 

Note that in the first few pages of the story, the devil remarks that he knows Brown's ancestors: 

I have been well acquainted with your family as with ever a one among the Puritans; and that's no trifle to say. I helped your grandfather, the constable, when he lashed the Quaker woman so smartly through the streets of Salem; and it was I that brought your father a pitch-pine knot, kindled at my own hearth, to set fire to an Indian village, in King Philip's war. 

The devil claims to have helped Brown's ancestors do these evil deeds. But in the fanatical Puritanical way of thinking, these deeds were done in defense of their strict understanding of religious practice. Clearly, Hawthorne is criticizing that Puritanical history of intolerance. Therefore, he is criticizing a group that would set fire to an Indian village simply because they have a different perspective on religious doctrine.