The primary defense that Bill Maher and Sam Harris use against the charge of bigotry against their assertions against Islam is that it is permissible to criticize an idea.
"Islam is an idea, not a race."
Well, yes. That's true.
However, not all criticisms of ideas are equal. Some criticisms have merit, some do not. Some criticisms are legitimate and others are not.
One source of illegitimate criticism is to confuse the idea with the people who believe it. There is a difference between criticizing utilitarianism, and criticizing utilitarians. There is a difference between criticizing creationism and criticizing creationists. When people blur these distinctions it is very easy to go from criticizing an idea to making prejudicial and discriminatory claims about people.
Particularly when your remarks attribute to the '-ist' a set of derogatory and denigrating attitudes that are not actually a part of the '-ism' you claim to be criticizing.
So, here are the rules for criticizing an '-ism'.
First, any claim that you are criticizing an '-ism' implies that you are criticizing a defining characteristic of that belief. It is something that defines whether a person is an '-ist' or not.
If a person says, "I am criticizing an 'ism'", and in the next sentence says, "Not all -ists' believe this," that person is speaking as incoherently as he would be if he were speaking about a bachelor and saying that the bachelor is married.
So, to criticize act-utilitarianism is to criticize that which defines a person as being an act-utilitarian. An attack on the proposition, "The right act is the act that produces the most utility" would be a legitimate attack against act-utilitarianism.
However, let us assume that an opinion poll shows that 99% of act-utilitarians believed in capital punishment. Even under these conditions, a criticism of capital punishment is not the same as a criticism of act-utilitarianism. The criticism would not count as a criticism of act-utilitarianism unless the criticism ultimately penetrates the specific application and attacks the underlying premise that defines one as an act-utilitarian - the premise that the right act is the act that produces the most utility.
In other words, if what you are criticizing is not a defining characteristic - if an '-ist' can still be an '-ist' even if he agrees with your argument, then a claim that you are attacking the '-ism' is false.
Second, be truthful about the representation of people who believe what you are criticizing in any group. If 'some' of '-ists' believe X, then say, "Some -ists believe X". If many '-ists' believe X, then it is quite permissible to say, "May '-ists' believe X". If a public opinion poll shows that, "74% if '-ists' believe X", then it is perfectly legitimate to cite the public opinion poll and say, "According to this poll, 74% of '-ists' believe X."
But none of this gives one license to say that one is attacking the '-ism' unless and until one's argument proves to be an attack on what actually defines a person as an '-ist' - where the very concept of being an '-ist' who rejects what is being criticized is incoherent.
Third, if criticizing a passage in the book or a statement that a speaker made, then cite the passage or the statement (and provide an accurate account of the relevant context) and criticize the passage or the statement. This is all that is needed. One's criticisms will automatically imply a similar criticism of anybody else who would agree with that passage or the statement as described in that context.
Fourth, when criticizing an act-type, focus on the act-type.
For example, I argue that the right to freedom of speech is a right to immunity from violence or threats of violence in response to words or communicative acts (such as pictures, gestures, cartoons, or the awarding of honors or awards). It is not, however, a right to immunity from criticism or offense - indeed such 'rights' would constitute a violation of the right to freedom of speech since they can only be enforced by violence or threats of violence against people for words or communicative acts.
In defending the right to freedom of speech - or condemning violations of this principle - it is sufficient to focus on the principle itself. It does not matter if one is a Muslim threatening to kill people who offend Islam, a liberal threatening to imprison somebody who argues that homosexuality is a sin, or a gamer using rape-threats to intimidate women critics of female representations in video games, it applies to all of these.
If one focuses on the act-type itself there is no risk of either over-generalizing (assigning guilt to people who are not guilty of the violation) or under-generalizing (letting off the hook 'allies' who are doing the things that you criticize but are not members of your targeted group).
These are simple rules to follow. They easily allow the criticism of any idea that one thinks is worth criticizing, but does it in a way that disarms any charge of prejudice or bigotry. It prevents any case of over-generalizing and criticizing people who are innocent, or under-generalizing and letting people of the hook who are guilty.
If somebody seeks to violate the rule - if somebody shows little concern over whether their words over-generalize and condemn the innocent or under-generalize and ignore the guilty - then that itself is a form of behavior worthy of criticism.