It's not clear from the news article whether the parent is a Christian who dislikes gendered references to their God, a believer in another faith that includes female divinities, or a non-theist who doesn't believe in divine forces. Without knowing what their specific objection is to the prayer, it's hard to comment on the news article.
However, according to this Website, the school in question is "a Mixed school of Non Denominational religion." If the Website is accurate, we're not talking about a secular school; we're talking about a school where, if the parent sends their child there, they know that the child will be exposed to religious practices. Again, without further information, it's hard to know why the parent chose to place their child there or whether they felt they had any right to input on such matters.