The problem with islam is actually very simple no matter how much some people 'muddle the waters' in lengthy posts in the hope that this will pass as a successful argument against the secular criticism of islam:
1. The basics of islam (quran + hadith + medival Islamic jurisprudence, still largely with us today) has many injunctions (explicit, clear meaning) in stark contradiction with Modernity. Muhammad's deeds are often very far from today's morality. The basics of islam may be amenable to some degree of interpretation but it is definitely not infinitely elastic in (rational) interpretation, no mental gymnastics can make some dark parts of islam disappear (other than by recognizing mistakes).
2. The quran however is viewed all over the muslim world as 'perfect' (pre-existent with god in heaven thus above historical criticism) and Muhammad as the 'perfect being' who deserves emulation at all times (this is what even the quran itself teaches explicitly).
3. At the same time unaided, rational,
Human Reason is severely played down in the muslim traditions, starting with the quran itself (after all islam means 'submission', people 'slaves' of allah).
That's why al Ghazali's views won so easily over the sunni world (unfortunately the shia are not far away in spite of a slightly better situation, this is why we have a theocratic iran and not a secular and democratic one, still too much reverence to the traditions). And the value attributed to Human Reason remains far from what it should be (in spite of centuries now of exposure to Modernity) to really make islam fully compatible with Modernity (via the transformation of islam, the only real option, going well beyond the mainstream islam of today). Finally usually those aware of the limits either prefer to hide or make sure that their proposals are modest enough to not be called 'apostates' (they are what I call passive carriers of the same islam of the past; in contrast the vast majority of more progressive muslims are unaware of the basics of islam, they are unconscious carriers of the same old islam which they never really challenge at the core).
4. The consequence of these is that in the muslim world it is still religion (islam) that strongly shapes culture and not the other way around (as in the other parts of the globe), no surprise that the level of secularism and liberal democracy is way lower than what is needed for the creation of really modern states.
There is a difference of degree here between the 'radicals' and many peaceful muslims indeed but sadly not of real substance (what even many of the 'progressives' of islam advocate fall way too short from what is needed to create a real and durable muslim Enlightenment). The outcome is much of the same: severe curbing of personal freedoms and free inquiry which put huge brakes to progress.
5. This brings naturally the next point, we have to use the same standards when defining who is moderate and who is radical / conservative in islam. A reasonable standard is that used to define moderate Christianity, the public attitude toward the status of the holy book and secularism is crucial for only rationality at this level, seconded by a healthy religious education can push the religion beyond a certain threshold of 'no return', that is a return, be it partial, toward the 'dark' practices of the past appears implausible. The cutting point is not between terrorists and peaceful but between those advocating publicly a healthy level of secularism + modern values + openly admitting that even the holy book is fallible and those falling short of this.
I'm afraid many muslims are not moderate in the western standard, including many of those considered 'moderate' today in the West (they never confront publicly sharia, preferring instead to claim that it is fully compatible with Modernity, or the view that the Jews are 'pigs and monkeys' and so on).
I do however make an exception for those like
Tawfiq Hamid who, while not advocating directly that even the quran is fallible*, let us read clearly 'between the lines' that he is fully aware even about its limits (we deal with moderation in the Western sense, at the very limit; at the same time we must never forget that even he is labelled 'islamophobic' by muslims and their western defenders). The real moderates at the practical level are limited to a few elites at the moment. there is still no moderate islam.
7. Finally the 'others do the same' 'argument' is a red herring, those who know well the basics of Christianity and Judaism know equally well that there is an important difference between the basics of these religions and islam, enough to produce significantly different outcomes at the practical level.
For example the fact that Christianity had since the beginning a bent toward interpreting symbolically the Old Testament and Jewish Law (and gives much more support pro the value of the unaided human reason**) than islam lead naturally to an expansion of what should be interpreted symbolically or contextualized historically (ever since Reason was rehabilitated in the 13th century) and finally made easy the 'quantum jump' to the view that at least sometimes the conclusions of the unaided Human Reason are more important than what is written in the holy book. As I said before it is not that difficult to remain a Christian whilst still accepting that the Bible is far from being 'perfect'. Sadly the particularities of islam make this jump extremely difficult.
*it is clear that he's forced by the very reactionary basics of islam to not make explicitly this step
**after all Job argues with God when he think he was mistreated, people can know what is good and evil via reason in Christianity and Judaism (unlike the theology of islam where submission is the only option, whatever god defines as moral via the holy book and muhammad is necessarily good)