Chapter 13 of the Vindication contains several of Wollstonecraft's most pointed commentaries on religion.
Earlier in the book, she has mentioned the rituals in the Established Church that she regards as "relics of popery." In her view, the instructors at colleges and public schools (i.e., what Americans refer to as private schools) are adherents of this superficial, ritualized aspect of religion. The young men who attend these institutions are corrupted in some sense by the hypocrisy of the teachers. This, in turn, bolsters the entire social dynamic in which women are disenfranchised and mistreated. It's unclear at this point whether Wollstonecraft is criticizing merely the trappings of religion (as dissenters from the Established Church had long done) or is criticizing religion itself.
In chapter 13, she asserts that many women, especially, have been preyed upon by men who claim to have the ability to tell the future and to work miracles. In her view, this practice is a direct contradiction of Christian belief and the concept of a single, all-powerful Deity. That women have been so duped is an indication of men's having attempted to keep women in a state of ignorance and credulity.
But Wollstonecraft extends this into an argument that seems to question one of the main elements of traditional Christian belief. She finds it strange that men should believe that a just God would punish souls for any purpose other than to reform them. The concept of eternal punishment makes no sense to her.
Wollstonecraft anticipates, to an extent, the arguments her contemporary Thomas Paine would put forth a few years later in The Age of Reason. However, her assertions are focused more directly on superstition as an element of the oppression of women rather than attacking Christianity itself.