The Inquisition was aimed mainly at lapsed Catholics, an attempt to stem the dissolution of the Church by "heretics." But whatever its roots, I ask you the last time you saw an Inquisitor hijack an airplane and fly it into a building. Or slaughter a bunch of commuters on a London bus. Or murder children in a theater in Beslan.
You can compare the predations of Christianity to those of islime all you want, but one was then, the other is now. I'd trust my life with a group of radical Baptists long before I'd trust it with a pair of "mainstream" muslimes.