Look beneath the surface of any major organization in this world, religious or laic, and you'll find that some of its adherents are less than sterling characters.
While individual Christian sects conduct protests outside of abortion clinics, and campaign for the election of candidates who advocate a Christian lifestyle, acts of violence against other religions or the ungodly are considered by the vast body of church-goers as aberrations to be condemned.
As to the Inquisition, it was aimed as much at critics of the Catholic Church hierarchy as it was at Jews. The criticism of the Church and its monetary and ethical corruption predates Martin Luther, and has its origins in leaders such as Jon Huss of Bohemia and Jerome of Prague, both of whom were excommunicated as heretics and executed by the Church.
The Protestant Reformation, and the wars fought in northern Europe to protect it from Church retribution were watershed events in Christianity. The failure of the Church to rein in the Protestant movement forced it to look inward and address the faults that had led so many to abandon it. The Counter-Reformation that resulted was the beginning of the end for militant Christianity.
Arising six centuries ago, the Reformation put Christianity on a long, often side-tracked path toward greater tolerance for, and acceptanace of, differing religious beliefs. Individual Christians or Christian sects might differ in attitudes about particular beliefs and attitudes, but the walk down that path continues.
Unfortunately, Islam has not undergone a similar movement. Until it does, the persecution of others of different faiths, the violence, the stoning of women, will continue.
