At least according to the BD novella, Ygerna was executed for helping her necromancer father perform experiments on children for the Black Ring. She had taught Damian some magic and tried to start awakening his powers, but had not told him about his origin when she was executed. The Black Ring ordered her to do so, but she hated them for how they treated her father.
As Stabbey said, executing Ygerna for her crimes may not have been entirely warranted considering she was acting on threat of death for herself and father, but she did still kill people.

can someone sum up the story

As for the consequences, Ygerna predicted that Damian's powers would not remain dormant for much longer, and that when he learned of his origins and Ygerna's execution he would hate the Divine for it. Lucian conceded that Damian wouldn't understand the need to execute her, but would forget about her in time, and continue with his life and teachings with the paladins. He hoped that Damian could still be prevented from turning into the Damned One.


In the past and currently, there are lots of situations where the actions of one or more individuals provoke a reaction against an entire group, or when arbitrary problems are simply blamed on a specific group, and any members of that group are suitable targets. The fact that Rhode was a zealot and that the humans at least forgot about the Black Ring when they withdrew and focused on dragons may be illogical, but is hardly unbelievable.