Do we prevent somebody being hurt by superstition or faith by rejecting and challenging those things? 

Is it mistaken to support organised religion in membership or donations?

If people do good because they are human, not because God prompts them then is it right to risk giving God any credit when they alone own their good?


Unpacking the not all bad view
When members of a religion do grave harm, people point to the religion and say, "It's people are not all bad. There are many good members."  This does not justify the religion.  It justifies the good people.  Yet they seem to mean the religion is good in itself.  That is insulting when you think about it.
Translation: "You have to know a person before you can call them good. Until then they are at best civil. But I will whitewash religion."
It is hardly a great thing if people have to be that fake in order to defend religious people! Is religion worth it if it demands and leads to that? No.
Translation: "Judge religion only by the good members."

A totally unfair and useless argument. If religion thrives on such nonsense and hypocrisy then it is proof that it is intrinsically bad. If you are really good, you will not ignore and thereby enable bad people. Christianity in particular likes to say that you show and draw others to the faith by the good works you do as a believer. It is strange to argue that good works show what the religion is like and the bad ones do not.
It makes no sense to judge primarily by the good members for goodness has a lot of motivations and a religious one may not be the main one for most. Judge them as people not as religious people. An evil religion has to have good members - that is human nature. It makes no sense to judge primarily by the good members when people die over the religion or when the religion does more harm than good in the long term. And what about the harm it does indirectly through hate of truth and bad example and what about the subliminal harm? Indirect harm is not made okay by being indirect. Sometimes it is worse and better at evil than direct harm. It is harder to identify which makes it very dangerous.
Translation: "We will ignore the fact that religion can't be that good if it really can be used for evil."
How much evil has to be done before anybody ditches the not all bad argument as a justification for the existence of religion? No religion tells us to ask that and yet religion has the nerve to use the not all bad argument as a promotional tactic. A religion that is happy that there are two good people in it when it has two billion members is not a good religion. It should be scrapped.
Translation: If the religion has bad people, so has every organisation whether religious or not.

That is admitting then that religion has no special or intrinsic goodness! The not all bad excuse should be used to defend people in general and not people as religious people.
Translation: The religion may be bad and have dangerous dogmas it will not change but we have to remember that the good people in it pick and choose.
It is obvious that if you have religious beliefs you should be in a body that supports you in them. The more lofty the spiritual aims you believe in the stricter you should be about being in a supportive religion. A religion is a collection of believers not cherry-pickers. It is believers who create the religion and invite new members. If you can pick and choose then why bother caring what religion you are in? If a religion is really for you and really good you will not feel the need to cherry-pick. Accepting God or the Bible as an authority and then picking and choosing is not really accepting them. You are the real authority not them when you cherry-pick. Cherrypickers are hypocrites who won't admit what they are - hypocrites. Religion may be bad but it is no answer to cherry-pick it while pretending to be loyal to it. Cherry-picking Nazi beliefs if you are in a Nazi group does not make you a good person even if your beliefs seem harmless. People will look at you and reason, "If I join the group I will not be a hypocrite like him. I will really support the group instead of pretending to myself that I really support it." Cherrypicking is a sign of a dishonest person and a bad or possibly bad religion. A really good and trusted religion will not be cherry-picked by decent people.
Religion is hardly credible when it uses the not all bad excuse! The excuse is not only useless, it is wrong. The more people in a religion who are bad by the religion's standards or by civil law standards or society's mores the more deplorable the excuse is.
When a religious group is harmful, those who argue that their religion does not matter are merely hypocritical enablers. Of course it matters!

The hypocrisy
Violent man will leave his mark on the religions he invents. Christians who show you the nice bits of the Bible and who ignore the bad or give them insufficient attention are honouring violent man. They are covering up for him.
Many like to argue that nasty religions are in fact misunderstood or good as if pretending that these lovely things are true long enough and hard enough will make them true or soften up the hard hearts of the terrorists.
If the religion is man's invention and gets some things right by luck and not because it is guided by God then the religion itself has to be bad in the sense that human nature is bad. The not all bad excuse utterly fails. It does the opposite of what it is intended to do. A man-made religion is doing bad when it preaches and prays for it is doing what man wants and pretending it is not and that it is evil to treat man's word as God's word. The religion prefers to do evil but in such a way that it looks okay or even beautiful. Outright evil is repellent. But those who enrobe evil in beautiful garb are to blame for those who do more obvious evil. They in fact have no business condemning them.
A religion is regarded as "not all bad" by outsiders because the insiders like to claim to be not all bad.
They do not dare say that the bad ones are good nearly all the time! They are hypocrites. If the not all bad excuse works then why don't religious people praise the bad ones as being good most of the time meaning that their bad does not matter very much? Why the double-standard?
They have suspicions about other religions and keep a polite and sometimes hostile distance. If you don't take "not all bad" seriously with other religions then why do you manipulate and expect people to take it seriously with yours?
Not all bad doesn't mean much when coming from a religion of hypocrites.
The not all bad view has awful consequences at times. Through immigration being too liberal, dangerous religionists for example have got into the United Kingdom.
The worst form of the not all bad argument is that, "My religion is not all bad and I am in it because everybody else seems to follow it." Copying others is no reason to be in a religion.  You do loads of good but you have racist views.  Against the grain you still help most people of other races who you meet.  You are not great if you are racist period. And you are not great if you think racists are brilliant. Clever racists mix good deeds into their evil to make their evil thrive.  That is the crux of the issue.  That is why you are to be severely condemned for light condemnation only plays into your hands.  It does not matter if you are deliberately doing good to lubricate the wheels of racism.  What matters is that you are doing it and you need to be awakened.
The other problem with not all bad is that it abuses religious labels. People fight as much over religious labels as they do religion. They use labels to put themselves in a box and to create an us versus them outlook. 

The reason we should not say, "Some members of that religion are bad not all" is that if the existence of the religion means one person is dead who needs not be dead then the religion is not worth it.  You cannot use the good members as an excuse for overlooking that.  See how serious this is.  This logic applies to religions that claim to be about doing good works but even more so to ones like Catholicism that prioritise rites of passage and end up with loads of members who have no commitment of love to their neighbours.

Not all bad is not the point.  It is seriously bad to say it is. The religion needs a through examination which may involve asking members to leave it.