Unfortunately Islam is indeed a religion, although some of its core writings do indeed appear to condone the killing of apostates (Moslems who renounce their faith). Other writings divide the world into the world of conformity to Islam (dar al Islam) and the outside world of "struggle" (dar al harb), and that the destiny/role of Islam is to convert the world. That has been interpreted by some adherents of Islam as authorizing the killing of "unbelievers", and indeed a great deal of the rapid expansion of Islam in the 7th and 8th centuries was accomplished in just this way. (Contemporary Christians preferred to convert the leaders of new nations and territories and through them, their followers (although that usually involved an element of force as well.).
I think the main difference is that the Christian/Western world learned in the Modern era (after the 14th century) to accept the preeminence of secular rulers as distinct from religious rule, though even there, a few more centuries were required to make tolerance of other Christian sects widespread throughout the Western world. Very little of that evolution occurred in Islam. A very powerful element motivating the original settlement of North America wat precisely that effort to find religious toleration.
Today most Moslem countries severely restrict the religious freedoms of non Moslems, and I believe we would be wise for us to amend our immigration laws to severely restrict immigration of prople from these countries, for precisely that reason. Such a rule would have prevented all of the 9/11 terrorists from entering this country. It would also create pressures on these countries to amend their practices and in particular pressures on any seeking to gain entrance into this country to affirm and demonstrate their adherence to our values.
I suspect we already have some level if infiltration of some of the more radical Islamist sects in this country. What we need is a more active program to deport those whom we suspect of radical affiliations. Aliens have no intrinsic right to remain here, and we have considerable discretion in choosing whom to allow to remain and whom to deport. We should be more vigorous in nthis area.