South Louisiana here. It can be used affectionately (seeing a sick child and saying Bless your heart) but I find it is more often used to point out someone's lack of intelligence or bad behaviour (Karen is pitching an absolute fit in the checkout lane at Albertsons because she misread a price label...Bless her heart)
Maybe you're from a more polite area of the south, but where I am we are heavily into calling out morons.