I think I understand what you're getting at here, but Im afraid the answer is going to be one of those "its a veeeery problematic question" kinda things.

What exactly are you asking about? How does history tell us otherwise? Are you talking about perceptions of Muslims by the west, in that Islamophobia is a new phenomena (I would argue that it is not)? Are you referring to the "Islamic Golden Age" of the Early and High Middle Ages? What I think the question boils down to is: How was Islam different in the past than today? More importantly, what is it about Muslims today that is different from in the past?

I think its important to ask, exactly what Muslims are we talking about? All if them? Because thats about 23% of the world population, 1.6 billion people. Each of those 1.6 billion has his own opinions on his religion. Even disregarding the individual's opinions, the number of subdivisions, as in any religion (Christianity, Bhuddism, Hinduism, all of them), is staggering. There are not just Sunnis and Shiites, though this is the largest major division; in terms of only Sunnis there are four different Sunni legal schools, the Salafist movement, Sufis, Wahhabis (though they wouldnt accept that term), Deobandis, etc. etc., heck, the list could go on for as long as you want. Even lumping some of these terms in as a distinct belief system is problematic. Shiites have just as much diversity in their beliefs, legal schools, and practices. Islam is practiced differently in South Asia (where the two countries with the largest number of Muslims, Indonesia and India, are located) than it is in the Middle East, or Africa, or Eastern Europe.

To sum it up, the differences between Islam today and Islam of history is....nothing? Everything? How different is Christianity today and Christianity of history. What are the differences between the Christianity of a 16th century Anabaptist and a member of the Westboro Baptist Church? Would a 6th century Gnostic recognize an American tent revivalist movement as Christianity? If you were to ask something less general, it would be easier to answer; something such as "Where do groups like ISIS or Al-Qaeda derive their theology?" or "Is there a historical precedent for strict, fundamentalist Islamic groups?", etc. But basically, Islam is as huge and diverse as any religion and it cant really be generalized too much.

In terms of reading more, I would look into some intro to Islam books. However, in terms of something which I think explores the issues that youre actually asking about, which would be the rise of Islamic extremism from a more theological point, would be Reza Aslan's "Beyond Fundamentalism: Confronting Religious Extremism in a Globalized Age". Like much of Aslan's work, it has its problems and is perhaps to simplistic, however its not a bad introductory primer. In terms of exploring the diversity of Islam, I cannot more highly recommend "Images of Muhammad: Narratives of the Prophet in Islam Across the Centuries" by Tarif Khalidi. Khalidi is in my opinion one of the best Islamic scholars in the world and has translated my favorite version of the Qur'an. In this book he details how the prophet has been depicted in various Islamic cultures and really shows the diversity of opinion, debate, and openness that can and does exist in the Islamic World.