Great article showing how the practice of questioning God is in fact well supported by the Bible.
Another story that comes to mind is that of Jacob wrestling with God, and apparently even winning (on some level).
Genesis 32:22-32Common English Bible (CEB)
Jacob wrestles with God
22 Jacob got up during the night, took his two wives, his two women servants, and his eleven sons, and crossed the Jabbok River’s shallow water. 23 He took them and everything that belonged to him, and he helped them cross the river. 24 But Jacob stayed apart by himself, and a man wrestled with him until dawn broke. 25 When the man saw that he couldn’t defeat Jacob, he grabbed Jacob’s thigh and tore a muscle in Jacob’s thigh as he wrestled with him. 26 The man said, “Let me go because the dawn is breaking.”
But Jacob said, “I won’t let you go until you bless me.”
27 He said to Jacob, “What’s your name?” and he said, “Jacob.” 28 Then he said, “Your name won’t be Jacob any longer, but Israel,[a] because you struggled with God and with men and won.”
29 Jacob also asked and said, “Tell me your name.”
But he said, “Why do you ask for my name?” and he blessed Jacob there. 30 Jacob named the place Peniel,[b] “because I’ve seen God face-to-face, and my life has been saved.” 31 The sun rose as Jacob passed Penuel, limping because of his thigh. 32 Therefore, Israelites don’t eat the tendon attached to the thigh muscle to this day, because he grabbed Jacob’s thigh muscle at the tendon.