Most often the accusation that God is cruel because of what is written in the Bible refer to the Old Testament passages where God kills or endorses the killing of women and children and even on occasion endorses rape and slavery.
Clearly the Noachian flood and the destruction of Sodom and Gomorrah, which according to the interpretations of creationists, came directly from the hand of God, would have resulted in the deaths of many innocents, particularly young children. But some passages in the Bible are rather shocking in their endorsement of cruel actions. Here’s Judges 21:10-24 [NIV]:
So the assembly sent twelve thousand fighting men with instructions to go to Jabesh Gilead and put to the sword those living there, including the women and children.  "This is what you are to do," they said. "Kill every male and every woman who is not a virgin." They found among the people living in Jabesh Gilead four hundred young women who had never slept with a man, and they took them to the camp at Shiloh in Canaan.
 Then the whole assembly sent an offer of peace to the Benjamites at the rock of Rimmon.  So the Benjamites returned at that time and were given the women of Jabesh Gilead who had been spared. But there were not enough for all of them.
 The people grieved for Benjamin, because the LORD had made a gap in the tribes of Israel.  And the elders of the assembly said, "With the women of Benjamin destroyed, how shall we provide wives for the men who are left? The Benjamite survivors must have heirs," they said, "so that a tribe of Israel will not be wiped out.  We can't give them our daughters as wives, since we Israelites have taken this oath: 'Cursed be anyone who gives a wife to a Benjamite.'  But look, there is the annual festival of the LORD in Shiloh, to the north of Bethel, and east of the road that goes from Bethel to Shechem, and to the south of Lebonah."
 So they instructed the Benjamites, saying, "Go and hide in the vineyards  and watch. When the girls of Shiloh come out to join in the dancing, then rush from the vineyards and each of you seize a wife from the girls of Shiloh and go to the land of Benjamin.  When their fathers or brothers complain to us, we will say to them, 'Do us a kindness by helping them, because we did not get wives for them during the war, and you are innocent, since you did not give your daughters to them.' "
 So that is what the Benjamites did. While the girls were dancing, each man caught one and carried her off to be his wife. Then they returned to their inheritance and rebuilt the towns and settled in them.
 At that time the Israelites left that place and went home to their tribes and clans, each to his own inheritance
The Benjamites killed and raped an entire town and then wanted more virgins, so they hid beside the road to kidnap and rape some more. There is nothing in the Bible indicating that God had a problem with any of this.
If these passages are factual accounts of what happened, then surely God is cruel.