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Mr. Murry enters the story three quarters of the way through the novel. Until that point, he exists in Meg's childhood memories as the father who called her affectionate nicknames, played math games with her, and assured her that everything was going to be all right.
With this childish image of her father as a superhero, the real thing seen through more mature eyes is bound to disappoint. Meg thinks all she has to do is find her father, and then he'll fix everything.
This was the moment that meant that now and forever everything would be all right.
As she pressed against her father all was forgotten except joy. There was only the peace and comfort of leaning against him, the wonder of the protecting circle of his arms, the feeling of complete reassurance and safety that his presence always gave her. (9.42-43)
Meg trusts in her father's power absolutely; to her he's Superman, capable of conquering any threat. Or, to put it another way, she sees him as the good version of IT, the higher power to which she can turn over all her responsibilities and relax worry-free.
But, like IT, her father's ability to play the role of savior is problematic. What Meg sees as her father's slowness to understand the situation with Charles Wallace begins to chip away at her image of him, and then that image is blown to pieces when Mr. Murry leaves Charles Wallace in the power of IT in order to save Meg. As part of Meg's growing-up process, she has to learn that these actions are not betrayals on her father's part of her faith in him, but rather that her father is a real person with faults who nevertheless loves her and wants to protect her.
Mr. Murry's transition from father-king in exile (hello, Shakespeare again) to human being is the meat of his character development; realizing this transition is key to Meg's coming to understand the need for her to take responsibility over her circumstances.