It's very freeing to be independent. I used to love the George Carlin line, "Never join a group that has a name." But I've learned that groups can perform positive and negative actions, and the consequences for the affiliated individual and for society in general differ accordingly. Some can be very grave. Some can be very positive. Institutions can do different things under different leaders over time as well.
Socializing in groups makes us who we are. There was a great and fevered debate between biologists Edward Wilson and Stephen Jay Gould as to how much evolution influences social behavior. Yet in his book The Hedgehog, the Fox and the Magister's Pox, Gould noted that he defended Wilson from a series of what he thought were unfair criticisms. Even these bitter rivals, representing opposed groups, could find common ground in their love of the study of life.
When it comes to religious disputes, I am a firm believer that they don't really exist. That is, I think the motivation behind religious wrongdoing has much more to do with political power plays than creed or doctrine. Author Moises Naim sees clearly the political contexts that religions grow out of. He writes in his book The End of Power, "With Islam, for instance, political factors make certain tendencies (Sunni versus Shia, or Wahhabi versus more liberal interpretations) dominant in different Muslim countries."
Without demonizing certain groups, it is possible to hold them to account when they do bad things. When they do atrocious things, the strongest condemnation is appropriate. One thinks of the Nazis and how many of their members claimed they were just following orders and how justifiably little pity the world had for that excuse. One can also think of the inner sanctums of secretive political-religious groups. I would imagine many followers who are less connected know little about how these groups work on the inside but identify with them based on their outer facades.
The Buddha said to be a light unto oneself, to rely on one's own judgment as the final arbiter, not what he supposedly said (which is a koan in itself). And Kafka wrote, "Anything that has real and lasting value is always a gift from within." Again, the problems come from those who distort their religious imagination to perform violent or unscrupulous political actions in order to gain advantage over another individual or another group. People who can think for themselves seldom get caught up in such horrors.
When we can begin to see group interactions in terms of power relations and not confirmations or denunciations of doctrinal purity, we may find some interesting things. For instance, the facts on faith and science are surprising. While some report that more than 90 percent of scientists are atheists based on their affiliation with the National Academy of Sciences, 2009 surveys by Pew, an internationally respected opinion poll, found that 51 percent of scientists believed in some sort of higher power, even if that conception of God is vague or spiritual. Why would a certain group of scientists and writers (the New Atheists) try to emphasize scientific lack of faith? To enhance their own group's power. Yet religion isn't going to go away, to the New Atheists' chagrin.
So to answer the titular question I posed, generalization of groups is usually wrong. However, it can be justifiable, in my opinion, to inveigh against the leaders and participants in a group's morally corrupt actions. When the power of a group or groups is used against another in a way that is meant to do harm to members of another group then you have just reason to impugn. Those consequences involve violence, oppression, lies and torture--no longer bingo night or the fish fry. Then it is no longer an association of individuals of good will and like minds peaceably assembling. At that point, those involved become some type of evil words can't wrap around.