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Arthur was a kid when he was crowned king at 14, 

He's a timid soul and easy to manipulate because of who pulls the strings, it's not that he doesn't have a backbone but it's because he's easy to take advantage of and manipulate, 

He's also a victim of SA, that really mentally fucked him over and filled him with disgust and shame apon finding out he slept with Morganna, his own sister, what would his people think of him? Worse than his father, and that put a lot of fear into him as well.

The age difference  as well, she was 17 and he was 14 when it happened.

and it doesn't help with how powerful Morganna is, she easily inflicted a curse apon him and made sure he wasn't gonna be having anymore kids to make sure Mc would be put on the throne. 

Her abilities are magnificent from curses to being able to change the storms of the weather 

And she's known for her temper and poisoning of those who she views as a threat, 

Arthur has a right to fear her, she's a big threat regardless