Recently John Piper wrote at the 
Desiring God blog an answer to the question, How Shall We Pray About the Upheavals in the Middle East?
In 1 Timothy 2:1–4, Paul connects prayer for “all who are in high positions” with a peaceful life for the followers of Jesus, and with his desire for all people to be saved.
First of all, then, I urge that supplications, prayers, intercessions, and thanksgivings be made for all people, for kings and all who are in high positions, that we may lead a peaceful and quiet life, godly and dignified in every way. This is good, and it is pleasing in the sight of God our Savior, who desires all people to be saved and to come to the knowledge of the truth.
There are two goals in praying for kings and leaders—that is, for political structures that exist, or might exist, in the Middle East.
1. We pray for political leaders and structures . . . “that we [the followers of Jesus] may lead a peaceful and quiet life godly and dignified in every way.”
J. N. D. Kelly comments, “In other words, not being exposed to the suspicion of disloyalty, they will be allowed to practice their religion without fear of disturbance and to lead the morally serious lives appropriate to it.” (The Pastoral Epistles, p. 61). That is one important thing we should pray for.
2. We pray for this politically sustained freedom and peace so that more and more people would be saved.
This is found in verse 3: “This [politically protected peaceable life] is good, and it is pleasing in the sight of God our Savior, who desires all people to be saved.” In other words, God approves of this kind of peaceable situation for believers (and the prayers that pursue it) because he wants more people to be saved.
The assumption is that a stable, peaceable situation in general makes for better long-term effective evangelism and missions. Very few persecuted churches that fear for their lives are mounting great global mission efforts to complete the Great Commission. As Philip Ryken writes in his commentary on 1 Timothy, “Peacetime mission is part of God’s plan for the salvation of the world, so pray for peace” (p. 63).
When we pray for the Middle East, we should be praying mainly for conditions to prevail that sustain freedom and peace for the followers of Jesus, so that the gospel would run and triumph, and millions would turn to Christ and be saved for his great glory.
Such conditions would include freedom for other religions too, since Christians do not spread their faith by the sword, but by proclamation and service (John 18:36).
Father in heaven, and Lord of all nations, rule over the Middle East in these tumultuous days so that political leaders and laws and practices are established that support peace and freedom for the followers of your Son. We praise you that you are not a tribal deity, and that you desire people of all ethnic groups to be saved through the blood and righteousness of Jesus Christ. In ways we cannot imagine, O God, govern the minds and hearts and systems and regimes and authority structures and intrigues and revolutions and constitutions and localities and neighborhood networks so that your people have protection, provision, peace, and spiritual power to lead holy lives, filled with fruitful passion to reach millions with the gospel. In Jesus’ name, Amen.
The Breadline 