1. Bilateral Covenants afford rights
After the conquest of Canaan, Joshua has an interesting proposition for the Children of Israel. Reflecting on their tendencies to fall into idolatry and syncretism, he says in Joshua 24:
“Now therefore fear the Lord and serve him in sincerity and in faithfulness. Put away the gods that your fathers served beyond the River and in Egypt, and serve the Lord. 15 And if it is evil in your eyes to serve the Lord, choose this day whom you will serve, whether the gods your fathers served in the region beyond the River, or the gods of the Amorites in whose land you dwell. But as for me and my house, we will serve the Lord.”
Non-unilateral Covenants - and this was a reiteration of the Covenant - are legal agreements in which each party surrenders certain things to the other in exchange for certain privileges. The 10 Commandments with which you are familiar is such a covenant - often formulated as "You shall be my people, and I shall be your God."
Regardless of whether or not as the Creator God already has a legal right over his people, God chooses to enter into a covenant with His people, thus affording them simple privileges.
2. Love is the desired thing - not obedience
Historically, theologians have attributed this to a problem of power disparity. As God, God has ultimate power to demand reverence and devotion, but in practice, this tends to overwhelm the less powerful party. Instead, God chooses to woo those whom he would have love Him - and requisite to taht would be both free choice and the ability to reject the suitor.
Jesus makes this explict in John 14:15 where he says:
"If you love me, keep my commandments."
As such, God phrases these as choices, in order to get what he wants - which is that sincere faithfulness which only comes from a free exchange.
Indeed, Jesus is often quoted against the Pharisses, but in one of his most damning indictments of disobedience, he tells them:
"Go and learn this saying - I desire mercy and not sacrifice."
Jesus is pointing them back to Hosea, wherein God reveals that his character is to love and to woo, not to overwhelm. In making such a god of the law, the Pharisees have perverted its purpose.
3. Judgement is coming, but love delays it
The Parable of the Wheat and the Tares in Matthew 13 is probably the best biblical support for tolerance. In the story, the enemy comes and sows weeds amongst good grain. When the farmhands discover this, they ask the master if they should tear up the weeds. The Master declines, saying:
‘No,’ he answered, ‘because while you are pulling the weeds, you may uproot the wheat with them. 30 Let both grow together until the harvest. At that time I will tell the harvesters: First collect the weeds and tie them in bundles to be burned; then gather the wheat and bring it into my barn.’”
Note that judgement will come to those who are not following the commandments - but the love that the Master has for his chosen compels him to afford all the opportunity to grow in love. Waiting until their fruits are fully known affords a time for everyone to come to love of the One who came "too seek and save the lost." Affording a chance to repent necessarily means affording a chance not to - thus allowing for some to reject God, but having the choice to do so in the first place.