There were no "millions of martyrs," except in the fevered brains of Protestant polemicists. We are not talking about the religious wars, but those who the Church deemed heretics and killed.
That stated very early and didn't end until the religious wars put an end to Rome's reign of terror.
Not to be snide, but Protestantism would have never survived if not for the Muslims (i.e. The Turks). Had the German Emperor not been distracted Luther would have ended up at a BBQ as well. Of course this is all 4-5 Centuries ago, and PJP II did apologize for these acts. I'm still waiting for the Queen of England to apologize for her ancestors raping, pillaging, enslaving, and starving mine all in the name of the Church of England (or Ireland as the case was). Let's not forget the South where in Virginia for a time one could not vote because of one's creed. I am sure the other southern states were equally as tolerant. We can go round and round on this or we can realize that it is the twenty-first century, and find bonds that bring us together. The alternative is bowing towards Mecca and worship of Allah.
Cheers,
CSG