Not everyone regards her as a villain. She's a bit more deus ex machina, with her own agenda. Personally, I'd rather follow her than an Inquisitor!
I, too, do not regard her as a villain. However, I don't agree that she is a true deus ex machina. Flemeth's character, even more than Morrigan, is integral to the story of Thedas and not simply a plot device to solve the problem of how one saves two Wardens from the hopelessly embattled Tower of Ishal nor how one gains Morrigan's loyalty and friendship. Her interventions have already had far-reaching consequences for at least two countries, if not the whole world.
With the dominance of the Chantry, we know so little of the time before the Veil. Even if Flemeth is merely a mage of incredible cunning and power, from Morrigan, we know shapeshifting requires close study of the animal form one shifts into, which would confirm Flemeth's prior association with at least one High Dragon, an association reinforced in The Silent Grove. If her agenda is to usher in an unending Dragon Age, what would that mean for Thedas?
While my personal tastes, too, tend against the Chantry and its associates, I would have to know what living under the Old Gods meant before committing myself to her cause. In Promethean fashion, it was the Old God Dumat who bestowed the Tevinter mages with the knowledge of blood magic. Why would a god give his followers this tool when other magic exists? l only oppose the use of blood magic when it requires taking the lives of innocent people without their consent, but I suspect it would be naïve to think the Old Gods did and would limit themselves thus.
If my theory is correct, battling or siding with Flemeth (once all her carefully maneuvered pieces are in place), who very well may be unto dragons as kings are unto ordinary men, will be a world-changing event and her defeat will be the only thing that can end the Dragon Age.