I think I may have phrased my original point poorly. I don't think calling a group of people ignorant is wrong if you mean the term in its literal sense of "Not having access to a certain kind of knowledge." And for instance as it relates to medieval people, you really are talking about a society in which decision-makers were usually very young and had significantly fewer resources to use in making their decisions, so you would be right. The problem, though, with deciding that any belief you don't like comes from a place of ignorance is that it seems like the "They didn't know what they were doing, but we know better now" people often seem to be the ones who become the most dogmatic and fanatical. When people start to either demonize or pity those they deem ignorant, it's a strong indication that they desire an easy way to dismiss dissent.
Europe used to be trapped in pagan darkness, but now we know better, and we know what the true religion is, so we should burn heretics whose presence threatens to undo all this good work and damn millions of souls. People used to have all sorts of superstitious and ignorant beliefs, but now, thanks to education and modern science, we're starting to understand how the world really works, and we have scientific proof that Jews and blacks are biologically inferior and must not be allowed to edge in on good white people. . . . Etc. etc. (I mean, as far as ignorance and hatefulness as primary reasons for evil go, it's worth noting that Germany prior to the world wars was one of the best-educated and least antisemitic countries in Europe.)
But also, I think there's really no point in trying to decide whether anyone else is right or wrong. I think the only thing you can do is settle on a principle you sincerely believe in and stick to it. You decide terrorism is wrong. Perhaps when you die, you will find out that the terrorists were right all along and you should have been slaughtering more infidels. But any God who would condemn you for not doing a thing you believed immoral is in my opinion no God at all.