After reading some of the claims listed on the site you linked to, I can conclude that there is an element of misinformation behind the content. And because there is so much of it, it would be unfair to expect me to sift through the material and provide a rebuttal for each claim. So I will direct you to a book which, if you sincerely desire the truth, should answer your question: http://islamicbookstore.com/b7626.html
If the Qur'an has never been altered, what about all the claims that it has listed here: http://www.answering-islam.org/Quran/Text/
The Muslim Perspective
Why do bad things happen to good people?
Answers: Atheist, Christian, Muslim, Hindu
Couldn't God have given us free will without giving us the desire to sin?
Answers: Atheist, Christian
Can you explain Naskh and izala within the Qur'an? What do these terms mean and do you accept their practice? Why or why not?
Isn't it the case that, rather than presupposing god as it claims to, the presuppositional view actually presupposes logic and reason?
Does the biblical god "YHWH" tempt? Because it says in Gen. 22:11 that God tempted Abraham, and in James 1:13 it says "God cannot be tempted with evil, neither tempteth he any man? Which should I believe?
Muslim Islam vs. Islamism: The Dilemma of the Muslim World Asghar Ali Engineer Muslim The Rights of Women in Islam Asghar Ali Engineer Muslim Islam: Misgivings and History Asghar Ali Engineer Muslim Islam: Religion, History, and Civilization Seyyed Hossein Nasr Muslim The Prophet of Non-Violence: Spirit of Peace, Compassion & Universality in Islam Asghar Ali Engineer Muslim Islam in Contemporary World Asghar Ali Engineer Muslim A Living Faith: My Quest for Peace, Harmony and Social Change Asghar Ali Engineer Muslim Welcome to Islam: A Step-by-Step Guide for New Muslims Mustafa Umar