The premises are false. First, you're assuming God protects from rape and murder. (He's not a real live protection spell.) That's called a miracle, because that is the exception to the rule. Most the time, the murderer or rapist murder and rape. But, no matter what happens it still falls under, Rom 8:28 - And we know that all things work together for good to them that love God, to them who are the called according to his purpose.
(And, I say that as someone who was raped as a Christian, so don't give me the traditional, "How can you be so callus" or the "But God is supposed to..." response.)
Second, you assume "free will" means our wills can let us do anything our minds want to do. Not so. Trust me. I really do want to swim to the bottom of the ocean, I will it, and yet, all logic dictates I can't.
Our will is governed by our nature. We can only will to do those things that are within our nature to do. That being said, God decreed that all that has/is/will happen happens. He's in full charge, despite our wills. No one wills to come to him, and yet some do. (Joh 3:14 And as Moses lifted up the serpent in the wilderness, even so must the Son of man be lifted up:
Joh 3:15 That whosoever believeth in him should not perish, but have eternal life.
Joh 3:16 For God so loved the world, that he gave his only begotten Son, that whosoever believeth in him should not perish, but have everlasting life.
Joh 3:17 For God sent not his Son into the world to condemn the world; but that the world through him might be saved.
Joh 3:18 He that believeth on him is not condemned: but he that believeth not is condemned already, because he hath not believed in the name of the only begotten Son of God.
Joh 3:19 And this is the condemnation, that light is come into the world, and men loved darkness rather than light, because their deeds were evil.
Joh 3:20 For every one that doeth evil hateth the light, neither cometh to the light, lest his deeds should be reproved.
Joh 3:21 But he that doeth truth cometh to the light, that his deeds may be made manifest, that they are wrought in God.)
ALL things work for the good of those called by God. By logic, one can only assume that means all things work out for the bad of the others. After all, God decided to create fish. Eons later, one of those fish descendants ended up swallowing Jonah all through "free will." Our will may be free, but ultimately all works out according to God's purposes, if we like his choices or not.