The witch hunts didn't last a thousand years in any one place, as far as I know. They began earlier in the southern Europe, moved north, and across the Atlantic, but also quieted down in the south earlier in turn.
Not really, they just got rebranded. While I wouldn't go so far as to say the majority of racism and homophobia has its roots in religion, its kind of chilling when the ultra conservative religous family members use the hard R word not five minutes after talking about how the "gays" need to be fixed in re-education camps. Then when they realize your in the room the conversation quickly changes to bake sales and who is going to be doing Missionary work in the godless countries. As I said, I'm not overly good with organized religion. The family really helped open my eyes to the real hypocrisy in their hippy trippy, Kumbaya bullshit. I'm just glad I'm a straight white male...
The number of victims, while tragic, was still a mere speck compared to the deaths caused by all the diseases rampaging across Europe at the same time, so people dying left and right was the norm in those times. Also, what does it matter if the religions are out of touch with distant past in such shameful matters? All the victims are hundreds of years past caring. We also know for a fact quite a good portion of the victims got accused for reasons that had nothing to do with any kind of witchcraft or pagan beliefs. People just conveniently got rid of others they didn't like.
Sorry m8, but because they are not openly burning witchs at the stake, or able to legally torture someone to death for their sins, hardly means the persecution, harassment, and act of violence are not carried out on a regular basis. And lets not get started on the travesty that is stoning and genital mutilation in Northern Africa and the Middle East.
It's easy to be ignorant when your so indoctrinated that you believe their lies that everything is ok, and you don't need to fact check or do your own independent research. But shit get real rather fast if you befriend wrong person or take up a hobby that conflicts with their religious views.