I'm going to have to disagree with your first point. Without any evidence (since this can't be measured) I believe that more evil has been done by religious organizations in the name of "God(s)" than for any other single reason. Money would probably be a close second. You know, stuff like the Crusades, the Inquisition, the Salem witch trials, the creation of the Islamic Caliphates, the holocaust (if you consider Hitler to be a cult leader), or suicide bombings. There are too many examples to name.
(Definitions for the purpose of this post: Logic and reason are the tools that allow us to understand the world. Skepticism lets us know when to apply these tools to scrutinize beliefs and ideas.)
My main objection to organized religion is that it encourages people to abandon reason. Since religious teachings cannot survive logical scrutiny (using the scientific method, etc.), they must discourage logic and skepticism. And this effect is total, since skepticism is an all or nothing thing. If you only question some beliefs and not others, then you are only going through the motions. And that creates serious side-effects that are invariably lethal for people who do not follow that same faith (and many that do). And if your are not skeptical, then you are likely to be suckered by one or more unrelated scams to the further detriment of yourself and society.
I tend to think of religion itself as a kind of memetic virus. It is infectious, can (and usually is) transmitted to offspring, it affects behavior, it resists attempts to remove it, and it mutates over time. I liken its discouragement of reason to the mechanism that HIV uses to prevent its removal by the immune system. A person who lacks the ability to accurately reason will not be able to reject the influence of religion, just as a disabled immune system cannot resist HIV (and eventually any other virus that comes along). I consider religious memes to be distinct from cultural memes, although historically they have been (and often still are) closely linked.
I consider organized religion to be a quasi-political organization that preys upon religious people and is symbiotic with religion as a whole. It tends to magnify the negative effects (war, persecution, etc.) of religion while also helping it to spread and compete against other religions. Religion can and often does exist independently of organized practice.
I also disagree with your assertion that people will only act altruistically if their moral code is buried in religious cruft. There are many ways in which moral values and cultural norms can be communicated to a member of society that do not involve religious indoctrination or the deprecation of [reason|skepticism].
Your second point is an example of the inevitable fact that everybody has some beliefs that they do not question. Nobody is completely objective, and everybody has been indoctrinated in somebody else's moral code and cultural norms.
Sometimes it is good - society could not function otherwise. After all, many people describe society as a shared consensus. The degree to which you share (or mimic) a culture's values controls the degree to which you can participate in the society.
Sometimes it is bad - when you condemn something simply because it runs counter to your own values and not because you have objectively evaluated it.
(As I look over the post, I find that I really don't think I have explained this very well. The virus analogy needs work. So I certainly won't be offended if you reject my reasoning. Indeed, I would be interested in reading a response)
The problem is not Islam, the problem is organized religion that encourages fundamentalist teachings and the abandonment of reason. Islam is not really more vulnerable to this than any other religion, it just seems that way because the fundamentalists' cause is buoyed by moderates who resent political persecution of 'the Islamic world' by 'the West'.
A perfect current events example of this is happening right now in Gaza. Before the 'truce' expired Hamas was largely considered a failed govt. by Gazans. A average terrorist group but a failure at running a state. If a new (and fair!) election had been held before the truce expired, Fatah would probably have won. But now, many Palestinians who despise hamas will still support them, because they hate the israelis far more and want to deny them a perceived victory.
I am not talking about morality or what the israelis should be doing, and I don't want this example to become fuel for a flamewar.
I'm just trying to point out a universal human characteristic: nothing brings disparate people together like a common enemy.
The perceived strength of fundamentalist muslims is not a religious phenomenon, it is a political one. This is a distinction that many people miss, IME.
While using a pigovian tax (aka 'sin' tax) is technically the right solution for this, care must be taken to plan for lost tax revenue when the tax works as intended. i.e. more tax = less gas sold = tax revenue drops just when the gov has gotten used to it. Since governments rarely plan for this properly (if at all), there will be a budget disruption with tax hikes (or borrowing, which is just a deferred tax) elsewhere. This happens unless the tax is spent solely on reducing the harm caused by the taxed activity. For ex. cigarette taxes that go to hospitals and lung cancer research. When people smoke less, hospitals need less money to treat uninsured smokers.
Its also a regressive tax, which presents its own problems.
While it sounds like a great idea in theory, it would basically be an unenforceable law criminalizing a victimless activity between two consenting people. It would be like prohibition (any type: drug, alcohol, literature, religious, etc.): totally ineffectual while simultaneously producing a vast amount of collateral damage.
Not that I haven't wished for similar tests (voting, political office, procreation, a real test for driving) in weaker moments... They all fail for the same reasons, unfortunately.
1 Sagan = Billions & Billions