A person can have negative things to say about a writer's current book yet still be a fan of the writer. Being a fan of a person's work doesn't necessarily mean that we are looking at it through rose-colored glasses.
Speaking as someone who's emailed authors to tell them I've enjoyed their work, I can say that for as much as you enjoy getting a positive email, we enjoy the fact that you respond back in acknowledgment. We're not looking to become best buds with you or encroach on your lives, but that simple act of acknowledgment humanizes you to a reader and builds up a tremendous amount of good will - good will that might tide you over if one of your next works is less than stellar.
