Now that the news is stating that Nidal Malik Hasan, the Fort Hood shootist, was a Muslim with strong religious convictions, I can already see the Bigot's Fallacy popping up in a number of atheist writings.
The Bigot's Fallacy begins with premises that are true of an individual or a group of individuals in a group, then suddenly leaps to conclusions that are applied to the whole group. A black man commits theft so then all black men are thieves. An atheist leads a campaign of genocide so atheism endorses genocide. A Muslim shoots a group of people in a Texas army base so theists are mass murderers.
The link that these bigots are trying to make is a belief that a God exists caused the agent to kill 13 people. Consequently we are supposed to fear and hate all people who believe that a God exists.
Typically, if somebody where to argue that A causes B, the presence (in America alone) of a couple hundred million examples of A and not-B would be taken as pretty good evidence that A causes B is not true - or, at least, that the situation is more complex than simple (minded) causation.
However, the quality that bigots share is bigots forego reason, If a fallacy gives even an illusion of support to a favored conclusion, then the bigot shuns reason and embraces the fallacy.
This might create a bit of cognitive dissonance if the bigot is also somebody who professes that rationality is a virtue and that people who shun reason for faith - or who otherwise embrace an irrational defense of a favored belief - deserves condemnation. However, this bigot avoids this problem with a display of hand-waving and cherry picking to give his use of fallacious reasoning an illusion of legitimacy that rivals the work of some of the best theologians and creationists on the planet.
Many of the people who embrace the Bigot's Fallacy in this case are quick to argue that nobody has ever done any harm in the name of atheism. The argument (the version that makes the most sense) begins with the premise that atheism is a belief that the proposition that "at least one God exists" is certainly or almost certainly false. This belief alone doesn't tell anybody to go establish a dictatorship and slaughter millions of fellow citizens. Therefore, it makes no sense to blame these atrocities on atheism.
The anti-religious bigot simply ignores the fact that the same argument applies to theists. The parallel argument begins with the premise that a theist is one who believes that the proposition that "at least one God exists" is certainly or almost certainly true. This belief alone doesn't tell anybody go fly airplanes into civilian sky scrapers or to murder people in a processing center at an army base. Therefore, it makes no sense to blame these atrocities on theism.
The problem, in the latter case, is a set of specific beliefs that one attaches to the belief that at least one God certainly or almost certainly exists. It has to do with beliefs about what that God wants. However, there are also belief sets that include the proposition that no God exists that are just as capable of motivating a person to establish dictatorships and promote mass murder. So, still, the two arguments are parallel.
Among the various atheist philosophies there are a few that put a premium on reason and evidence. Among members of that subgroup of atheists, there should be some way to introduce a moral objection to the Bigot's Fallacy and similar breeches of reason. These options are to be shunned - not because it is politically useful to be nice to theists, but because good people condemn the use of fallacious inferences in themselves and others.
Having said this, the Texas shooting does provide good reason, not to go after 'theism', but to go after any specific religious teachings that seemed to support the shooting, and any person who speaks for a specific religion who praises the shooting.
For example, according to the New York Times:
"He felt he was supposed to quit," Mr. Reasoner said. "In the Koran, it says you are not supposed to have alliances with Jews or Christians, and if you are killed in the military fighting against Muslims, you will go to hell."
Does this imply that, in a dispute between an unjust and violent Muslim and peaceful Christians, one must side with the unjust and violent Muslim? This is a view that is definitely worthy of condemnation. If anybody should then answer that if he rejects this he would have to reject all of Islam, the proper response would be to shrug one’s shoulders and say, "I leave it to you to work out the details."
This has nothing to do with claiming that there is some sort of virtue to be found in being nice to theists, or arguing that it should be done for the sake of political expediency. What I am talking about here is the virtue of sound reasoning and embracing the conclusions that reason and evidence supports. The problem with the Bigot's Fallacy as atheists use it, or the other inferences discussed above, is that they transgress the virtue of reason – and in doing so also transgress the virtue of justice and fairness to those who become the victims of unjustified accusations.