Many people were chagrined that Pope Francis met personally with Kim Davis, lending a patina of spiritual credibility to her odious mission of exclusion and bigotry. A close friend of mine found this a solid reason to dismiss him completely, calling him "a kinder, gentler bigot, but still a bigot."
I am an ex-Catholic atheist. I'm not an anti-theist, which I think is how atheists are seen by most theists (and to be fair, most public atheists like Richard Dawkins, Sam Harris, Bill Maher and the late Christopher Hitchens certainly ARE aggressively anti-theist). As a liberal and atheist, I was disappointed that the pope lent that awful woman credibility, but as an ex-Catholic, I was not surprised by it.