When we say that we believe that all things come from God, we are not saying that He causes all things and is the author of evil. The Isaiah passage above makes an important distinction when God says that He creates calamity and causes well-being. He has created all the elements and systems in the world, and He has allowed them to function according to their design and purpose. The greatest calamity in the history of mankind, the fall of Adam and Eve, occurred according to the counsel of His will, but it transpired because of three elements which He created––all of which were good and without which it could not have happened as it did. 1) He created man in His image with a desire to be like God. 2) He also created and gave Adam a law (without which there could be no sin), and then 3) He allowed the adversary, the devil, a being which He created and allowed to fall, to enter the garden at that time in history. With these elements in place, the Fall was a great calamity created by God, though not perpetrated by Him, and not without a purpose motivated by love, which was, through all of history to reveal the glory of God in and through Jesus Christ.
As for God’s statement that He causes well-being, think for a minute about the state of the world after the Fall. In order for any well-being to occur in a fallen world with men who are enslaved to sin, God must cause it, for we surely cannot! For God to cause any good in a fallen, hostile world, He must be motivated by love. Consider God’s assessment of fallen mankind, that “every intent of the thoughts of his heart was only evil continually” (Gen. 6:5), and Paul’s assertions that we are hostile, engaged in evil deeds (Col. 1:21), and unwilling to submit ourselves to God and His law (Rom. 8:7-8). With hearts so self-serving, self-seeking, and self-fulfilling, as well as so dismissive toward the One who has given us life in the first place, who can claim that they deserve to be loved, or to enjoy any good in life? Yet, while we were in this condition, God sent His Son to die for us, to restore the beauty of His image in us that was lost in the Garden, to destroy all the works of the devil, and to redeem and transform us so we can spend eternity with Him! This is God “causing well-being”!
So, to be clear, when we say that all things come from God, who is love, we are not saying He is the originator of evil. Evil and tragedy result from the fallen world, our fallen flesh, and the fallen angel Satan, who hates everything God has created, and especially humans, who bear His image. We can also say that God holds Satan and all men responsible for their deeds. This may be beyond our comprehension, but it is true nonetheless. I know of no greater testimony of this truth than Peter’s explanation of the crucifixion of Jesus to the men of Israel who put Him to death.