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Samuel Rutherford in Sermon 1 of the Trial and Triumph of Faith explains why we often do not understand what God is doing. First, we must understand that God’s Providence is complex: God uses even sin for His own ends:

The Providence of God hath two sides; one black and sad, another white and joyful. Heresy taketh strength, and is green before the sun; God’s clearing of necessary and seasonable truths, is a fair side of that same providence. Adam’s first sin, was the devil and hell digging a hole through the comely and beautiful frame of the creation of God; and that is the dark side of Providence: but the flower of Jesse springing up, to take away sin, and to paint out to men and angels the glory of a heaven, and a new world of free grace—that is a lightsome side of Providence

Second, we look upon only a portion of God’s work; it as of we judged the outcome of a story but stopped in the middle or sneered at house which was not complete;

—It is our fault, that we look upon God’s ways and works by halves and pieces; and so, we see often nothing but the black side, and the dark part of the moon. We mistake all, when we look upon men’s works by parts; a house in the building, lying in an hundred pieces; here timber, here a rafter, there a spar, there a stone; in another place, half a window, in another place, the side of a door: there is no beauty, no face of a house here. Have patience a little, and see them all by art compacted together in order, and you will see a fair building

We are impatient of our ease and want our heaven while we are upon earth.