While indeed there is the matter that 4000 killed for thought crimes in Spain alone is 4000 too many, also consider this:
Spain had a population of about 9 million when that madness started. Let's say 10 million or so average over most of the period (they never implemented effective quarantine measuared, and got whacked by the Black Death often and hard.) Also because it makes back-of-the-napkin maths easier.
By way of comparison the USA nowadays has some 300 million inhabitants.
Imagine that an organization had killed 120,000 US citizens. Because that's what that simple proportion works out to.
The USA went ape #### over 10,000 or so (again, rounded) in one terrorist attack, ditched constitutional safeguards, and attacked two countries over it. 120,000? Man, that would be some hating right there. Add them dying screaming in agony on top of a pile of burning wood, for anwwhere between 1 and two hours to die? Now that would be some being out for blood right there.
Or yes, let's talk about Germany. The 10,000 witches killed sound about right. Germany oscillated somewhere between 10 and 15 million for most of the burning times period. Let's take about 12.5 million as a median. Now, unless my maths are wrong, for a country like the USA today the equivalent would be something like 300x10,000/12.5=240,000 killed.
Can you imagine the kind of hatred if 240,000 Americans, the vast majority females, most of them kids and teenagers, got brutally killed in the name of ANY religion?
You can even split it across 200 years, which is about as long as the madness lasted. That's like more than a 9/11 attack every single year. Though it peaked between about 1580 and 1630, in which time it's more like the equivalent of two 9/11 attacks per year, put in proportion to population size. We talk about a heinous act of terror that the 9/11 even happened ONCE. Can you even imagine what it would mean to live in that 50 year period where you'd get 2-3 times as many deaths per year, every year, in the name of ANY religion? You think Al Qaeda is terror? Now wrap your mind around THAT terror campaign in the name of Xianity.
So, yeah, 4000 or respectively 10,000 is already 4000 or respectively 10,000 too many. But put it into perspective of the populations at the time, and, yea, you can probably see why apologies of it make me see red.