It could also be because of fear, and not just apathy and indifference. Look at things right after 9/11 happened and how few moderate Muslims stood up and denounced the terrorist actions. Many of them did not speak out because they were, and still are, legitimately afraid of the very violent minority in their religion. Or with your witchcraft example, fanaticism says that if you are sympathetic towards an oppressed group, then you must be one of them too. I don't think we will ever know the breakdown of those murdered in that purge who were directly accused vs those who just spoke out against it.
A couple of things. The vast majority of muslims in the west denounced the 911 attacks when you got to the middle east maybe not as much although as has been mentioned in other posts my knowlege is dependent on the amount and accuracy of reporting. (what they were saying in their own communities I suspect neither of us will know).
this does not necessarily disagree with what you said as you didn't specify but I thought it worth clarifying
In terms of reason I don't think you got it exactly right. Although fear is a part of it. it was more complicated than that, you do touch on this in your witchcraft example so again this isnt a disagreement as much as a clarification.
There was of course a famous declaration of "you're either with us or against us" from the POTUS at the time and of course radical terrorist groups are hardly interested in moderate debates critcal of both sides.
It meant those who were genuinely appalled by the terrorists but who also genuinely upset by the death meeted out to their compatriots often by western backed regimes with western supplied weapons get stuck with no recourse. Try to bring up the muslims who are suffering and you're labelled a sympathiser with terrorists. Support the western military response uncritically and you're saying the lives of people like you don't matter.
Better to hunker down and say nothing publically because you can't win.
This isn't a anti western diatribe the terrorists deliberately used real issues to try to legitimise their murder it wasn't all one way. There were people dying on both sides who didn't deserve to but each side was only interested in their own people to fit into their own narrative and didn't want any muddying of the waters.
If you look at the history of the Troubles in Northern Ireland you see exactly the same pattern. If you're not 100% supporting us you're with the enemy. And there, there was a much more real threat of some friendly neighbours in balaclavas coming to have a word with your kneecaps about "loyalty".
On witchcraft the funny thing is it came almost entirely from the people. Where there was strong authority the reaction to "she's a witch!" was "No she isn't now get back to the fields before we stab you." it was usually where there was weak or insecure government, often where there were rival authorities or overlapping boundaries where you got a populist race to the bottom to indulge the masses. "we are tougher on witches than that other lot!" kind of thing. No all badness comes from evil authorities ordinary people can be sh*ts too.