Rather than beating on these groups' modern incarnations for what their predecessors did, one should focus on what they are doing here and now, while also understanding that one subsection's behavior has no bearing on all the others.
So yes, Ponderin, extremists like the Taliban and Saudi Arabia have caused a lot of suffering and death among those they have influence over - but that doesn't mean that all Muslims are misogynist bastards, just like the Westboro Baptist Church doesn't stand for every Christian on the planet. And it certainly doesn't mean you should talk and/or think about them as if they weren't people, even when dealing with groups like Al Qaeda. After all, if you don't at least try to understand why they do what they do, how can you hope to defeat them? Worse still, if you just re-imagine everyone who disagrees with you into one-dimensional cartoon villains, aren't you running the risk of becoming just as draconian and heartless as you imagine your enemy to be?
Pol Pot, Augusto Pinochet, Hans Anders Breivik, and the Tonton Macoutes were able to commit atrocities in part because they had learned to think of those who didn't support their views as "bad guys" or "the enemy", instead of as people - and could thus harass, torture, and exterminate them without feeling guilt.
If you don't accept that you could be wrong, and don't keep in mind that everyone else has emotions, likes, dislikes, beliefs, and opinions of their own, then you lose the sense of empathy that keeps a man from becoming a monster.