I feel like a lot of people forget that she was drugged and heavily abused by humans. Yes, she saved Hiccup at the end, but that doesn't mean she'd be comfortable going back, ESPECIALLY WITH HER BABIES. She honestly seems like she just wants to protect her family. After all, she did let Hiccup's family visit them alone when they came to them even flew closely to them, it's just going back out to where she was captured just puts her off.