Most muslims are indeed decent people on most issues. So were most Nazis, most Crusaders, most catholics etc. John Rabe, a committed Nazi, saved thousands of innocent lives at personal risk to himself, during the Chinese massacres in Nanking for example. I am sure the average Nazi party member in Germany would have been a fairly friendly fellow, put you up in his house if you were lost or a guest, be square in his dealings with you, and so on. That does not make Nazism any less horrific an ideology, and that did not stop Nazi German society butchering tens of millions of innocent people. That did not stop the horrors of the Crusades or the Inquisition, did it? So, I think we can safely say that the day to day conduct of the average member of an ideological movement is fairly irrelevant.
The conduct of most muslims is completely irrelevant to the assessment of Islam as a doctrine, just as the conduct of most Christians is completely irrelevant to the assessment of Christianity as a doctrine, or atheist conduct has no relevance to the claims and credibility of atheism, or the conduct of mathematicians has to the claims of mathematics. What matters is what the doctrines command and claim. Islam commands that apostates (muslims who decide to change religion) be killed. Virtually all islamic scholars, including so-called moderates, support this position. That is a barbaric act. There is NO common ground between that belief, and the belief in liberty, and in freedom of religion. The Inquisition also held the same belief - presumably you would not try to defend the Inquisition and its supporters on the grounds that most Spanish catholics were pretty decent fellows in most other respects?
Therefore, any muslim must choose either to support the commandments of their religion, and support the execution of apostates, or they must reject and turn their back on that particular commandment of their religion - thus becoming, in part, anti-muslim in their beliefs and conduct. They must either accept islam and reject liberty and civilised values, or they must reject islam to at least some extent.
Attempting to say that we are all the same is to ignore this gigantic difference. Most muslims support execution of apostates. Most non-muslims do not. If you have any concern for the plight of innocent victims, this is a very important distinction. If you are an apostate, that is literally a matter of life or death. I'd say that is a pretty GIGANTIC difference in personal conduct and morality. Trying to whitewash this is just ignoring reality and turning your back on innocent victims of religiously-sanctioned murder and oppression.
It is always productive to criticise evil and barbaric actions - that is how you stoke opposition and eventually reform and positive change. Horrific things like slavery were not abolished by assuming the good nature of man, they were abolished because a few pioneers realised how evil it was, and worked with former or existing slaves to popularise this basic fact, and convince normal 'good-natured' people that it was fundamentally immoral. It took literally thousands of years for this to happen. I would say that abolishing barbarism and killing of innocent people is a VERY productive thing to do.
