there are legitimate concerns specific to islam that we should be able to talk about without bigotry.
True. There's certainly a lot of actual bigotry around, but in my personal experience the term "Islamophobia" tends to be thrown around a lot by people who don't like criticism of Islam (particularly by Islamists). People like Harris and Hitchens are often branded Islamophobes in order to taint their arguments as racist.
Far be it from me to praise Christianity (or any other religion), but Islam does have features that make it somewhat different from Christianity, in that it is highly politicized at it's core; Mohamed was not just a prophet, but also a political figure and a warlord. Unlike Jesus, he was a ruler who had to deal with the banalities of political life. Because of this, there is no obvious distinction between politics, culture, economy and religion in Islamic life as proscribed by the Quran and the Hadith, making the potential for politicization, fundamentalism and radicalization much greater. The history of Islam is
the history of the politics of the Islamic world. By contrast, although there have been times when the Christian church was a sort of rival of the European political elite, the two have traditionally been at least nominally separate. And a related issue is that, in contrast to Jesus' role as a non-political prophet, Mohamed's modus operandi inevitably came with a lot of violence, and was explicitly expansionist (more on this below). Islam is not pacifistic at it's core.
And there are other issues that render Islam more politicized by default. For example, in Islam, there is no such thing as "original sin". The first and second major sins according to Islam are thinking we as humans are self-sufficient (i.e.: that God is not needed), and idolatry (something, e.g.: money, graven images, pictures of God in human form, taking the place of God). Islam means submission to God (making even Christians and Jews who submit to God technically "muslim"), which is supposed to bring peace by averting these two sins. However, worshiping the law of man over the law of God is a form of idolatry, which is why Shari'a is supposed to always override man-made laws. Additionally, in the time of Mohamed, switching religions was synonymous with switching political alliances, which is why apostasy is seen as treason, to be punished by death (specifically, by burning, since apostates should be treated as if they are already in hell).
Another issue is the concept of abrogation. The Quran says that revelations are progressive, so that later verses override earlier ones (just like the revelation of Mohamed overrides that of Moses and Jesus). And Mohamed's life is often taken as exemplary, and to be mimicked as closely as possible, since he was, after all, their prophet. However, the history of Mohamed is one of progressively more violent, aggressive and expansionist behavior. He starts out as a peaceful preacher, but later takes up arms to defend himself, and then finally goes on the offense. He becomes a much more violent, less tolerant person, eventually turning into a warlord. By the principle of abrogation, this means that less tolerant, more aggressive, more expansionist, more violent verses tend to override more peaceful ones. So when Al Qaeda tells the Muslim Brotherhood to go from the Mecca stage to the Medina stage, they are referring to this process of abrogation and telling them to take up arms like Mohamed did during that stage of his life.
And of course, Islam claims to be the final, unalterable revelation (that can't even be properly studied in a language other than Arabic), effectively rendering reformation much more difficult.
Of course, many moderate Muslims find various ways around this, but (imho, from what I've read) it is one of the reasons why Muslims may radicalize more easily than Christians do, and why in many Muslim majority nations there is no clear separation between Mosque and state. Tawfik Hamid describes this in his book Inside Jihad
, where he talks about his own radicalization process. He notes that his Sufi teachers could only offer vague, feel good ideas about peace and loving others, whereas jihadists could point to exact Quranic passages and rely on relatively consistent ways of arguing. That made the Jihadists much more convincing to him, as a young devout Muslim trying to attain religious enlightenment (of course, there's more to it than that; they also use cultish socio-psychological leverage that could have come straight out of Margaret Thaler Singer's Cults In Our Midst