And a few short centuries ago, "Christendom" executed athiests, with the Roman catholic Church leading the slaughter.
Citation needed. If you point at the Spanish Inquisition, but even at that point in time, there were Jews and various Christian faiths and Muslims and freemasons (atheists/agnostics) living across the Western World. The Inquisition didn't end until the mid-1800s, at which point the US for example was already well established as a free nation, as were the British. Spain, the backwater of Europe, has always been a bit behind on those things.
Perhaps get educated about the Spanish Inquisition, about 2000-3000 people were killed at the hands of the Inquisitors over a period of 400 years, these were primarily political opponents of the pope (who then reigned as a king). Not excusing it, but just pointing out that it wasn't the eradication of muslims or the eradication of atheists at its goal, it was political persecution under the guise of religious idealism. And it also led directly to religious wars between France and Spain, the British and Spain, protestants and catholics which killed hundreds of thousands of people.
Today, these Muslim countries not only kill their political opponents, it is open season on everyone from gays to Christians, and if your daughter or wife gets raped, you have to kill them too, the Spanish Inquisition and even the most devout Christians never went that far.
Also, Muslims now have examples of how to do it right. To excuse their behavior now because thousands of years ago, others did the same is just plain evil. The developed world used to call those people "barbarians".