I wouldn't say she was a positive example of a female ruler...
I don't think the reason they didn't like Isabel and Gaston was solely because they were a woman and a Frenchman respectively(it didn't help, of course). They(especially Gaston) seemed to be disliked on their own merits, although I haven't seen much about it that would give me a better read of both personalities - D.Isabel was said to be an Ultramontane Catholic, something that was bound to clash with every Freemason out there(one of which was her father), not to mention with Brazilian policy regarding Catholicism(Church Edicts, including Papal ones, could only be enacted in Brazil by authorization of the Emperor), but that's the only thing I know.
Whenever I hear "Masons!", I think of conspiracy theories, to be honest.