Reverend Buckley is interested in Kit because her grandfather was knighted.  He is impressed by that, as it is a significant honor.  He asks her if she was a loyal subject of King George.

“So, young lady, your grandfather was knighted by King Charles, you say?  A great honor, a very great honor indeed.  And I take it he was a loyal subject of our King James as well?” (p. 60)

Kit doesn’t understand the question, because it does not occur to her to be anything else.  The reverend suggests that she needs to keep her loyalties.  Buckley uses Kit to insinuate that Matthew is a traitor because he is interested in protecting the rights of the charter.  He is suggesting that by living in Matthew’s house she would become a traitor.