For what I am about to say, you will need to see this video. Also, remember that I am a pastor, a Christian, and not at all interested in becoming Muslim. I find much of Islam's teachings to be problematic. However I do not like false-characterization of the ugliness of my own faith's history, nor false-characterization of the faith of others.
I would never justify the crusades. Having read a great deal about them in my church history classes, they are one of the worst things that Christians have partaken in. There is very little good about them, and all Christians should be deeply embarrassed by them. He skips such things as the children's crusade, the knights slaughtering Christians because God would sort them out, and the whole concept of fighting a holy war solely for the purpose of taking back the holy land. These were foolish, bloody, and there was very little holy about them.
Dr. Bill Warner distorts several facts. The motivation for the Crusades was not to free Christians. There was the desire to push back the Muslim offensive -- I will give him that, but always the desire was to take back the holy land from the infidels (both Muslim and Jews). Christians were seldom freed by the actions.
The armies left with little provisions. As the armies traveled they looted they Christian cities along the way, fighting and killing people to feed the armies. When they arrived, they were seldom acting to free others, but simply to kill all. One example, on July 15th 1099, Christians took Jerusalem. What followed was a horrible bloodbath. Women were raped, infants thrown against the walls. A synagogue in which many Jews sought refuge was set fire and they were prevented from escaping. The eyewitnesses say that the horses waded in blood.
Third, he only considers the official crusades, and none of the other battles which Muslims might consider acts of aggression. Nor other Christians offensives into other lands. The establishment of Israel could certainly be considered one. I have heard Christians talk about Gulf war, the war in Iraq, and the war against terrorism as religious wars. If Christians talk about them in that way, how do you think Muslims perceive them? Although we see them as defensive -- they take place in their homelands -- so they probably don't feel defensive to those whose soil they take place on.
He talks about slavery but ignores that Islam has very strict guidelines on the treatment of those slaves, including seeing them as human beings with certain rights. Consider the millions of slaves that Christians have taken from Africa, and it was justified because they were not Christian, the treatment was inhumane and there were few if any rights. What follows is a deep and lasting problem of race relations in the US. He doesn't mention lynchings of Muslims in many Christian countries, several within the last year (see the Central African Republic for one example). You can bet those Muslim extremists do consider those acts.
He also claims that there is no command to kill non-Christians in the New Testament. Close, but not quite true. Jesus parable of the vineyard in Luke 20 (also in Matthew 21) has been used to justify the killing of non-Christians. Revelation frequently mentions the armies of God killing large numbers of people, and often when people start believing that the end of times is near, they justify themselves by saying that they are those armies.
He also assumes that all Muslims consider Jihad to be a physical war. The term itself means struggle and often does include military battle. However, some consider it to be the internal spiritual struggle. And he assumes that it has a negative connotation; however some wars -- even most Christians would agree -- are against such evil that they are indeed necessary and part of the duty of the followers of God.
Before you judge the president's words at the prayer breakfast, remember that history is often an ugly thing, that much evil has been done in the name of religion, and that denying our own capacity for evil is one of the first steps to committing great evil. Yes, ISIS, is committing great acts of evil. But the crusades were as well, as I quote one crusader, who was bragging about the holiness of the soldiers in their treatment of the women that had been left behind in a Turkish camp, "We did nothing evil to them, but simply speared them through." And I could go on and on through history pointing out Christian brutality -- we must be willing to see the log in our own eye, before working to help our brothers and sisters with theirs.