There was no fighting between Shia and Sunni when Saddam was in power (I suppose he alone was doing enough killing for both). The infighting between Shia and Sunni started after Bush invaded Iraq.
So nobody is accusing Bush for killing half a million Iraqis (as I said before, USA does not set out to kill Muslims). However, USA does bear indirect responsibility for all the violence occurring in Iraq after the Iraq invasion.
Besides, Colpy may disagree, but I think Fundamentalist Islam is a bigger threat that USSR ever was. There was a balance of power (or balance of terror) between USA and USSR. Both were armed to the hilt, but nether dare attack the other, because they knew that whoever embarked upon the first nuclear strike will be paid back ten fold.
But here is the important difference between USSR and Taliban or Al Qaeda. USSR did not want their country devastated by nuclear war, so they did not attack USA. There was peace between the two for decades.
Al Qaeda or Taliban does not care if there is a hundred fold retaliation, they do not care if 100 million Muslims die as a result of US retaliation. If they can get their hands on a nuclear weapon, they will hit USA, hit it hard, and damn the consequences.
Possibility of nuclear warfare is greatly increased with Taliban or Al Qaeda, and in that respect, Taliban is a much more dangerous enemy that USSR (though perhaps not as powerful).
In World War 2, USA was shrewd enough to realize that Nazi Germany was a much more dangerous enemy than USSR. Unfortunately, they got things wrong in Afghanistan, they decided to support the wrong side (Taliban).