Whether or not any particular Muslim is intolerant of other religions is one thing. However, Islamic society and Muslim communities in general are intolerant of other religious groups, especially in countries where Islam is the dominant religion politically. There are several reasons for this:
1) Systemic "Religionism": In the US South in the 1980s, segregation was no longer legal, but the imprint of segregation was still felt in the south. Miscegination between Blacks and Whites was not really accepted and Whites generally had a negative attitude toward Blacks, even though they were legally equal. This is called Systemic Racism. It is is much the same situation in most Islamic Countries, but with religion instead of race. Historically, Jews, Christians, Sikhs, and Hindus under Islamic governments were second-class citizens and so the transition to making them truly equal partners suffers from this history. Conversely, very few Muslims (prior to the last 50 years) lived in minority-Muslim countries, preventing the development of an Islam without Systemic Religionism.
2) Qur'anic Injunctions: Of course, different Muslims interpret the Qur'an differently, but there are certainly Qur'anic verses that can be read by those seeking to be intolerant of good grounds to do so. Q: 3:19 claims that the only religion that is acceptable to God is Islam. Q: 3:110 claims that Muslims are the best people in all history. Q: 8:55 claims that those who disbelieve are the worst of animals. Q: 9:29 argues for the repression and inequality of Jews and Christians before Muslims. -- There are numerous other verses that promote the view that intolerance and inequality between Muslims and Non-Muslims is Divinely Supported, creating difficulty in rejecting it. Additionally, the Qur'an has numerous verses that are Anti-Semitic or Hateful towards Christians.
3) Denial of Intolerance: Most Muslims refuse to believe that they discriminate or harbor any animus towards individuals of different faiths. (There are some exceptions like Sheikh Hamza Yusuf who has noted that Muslim violence against Jews in the US is more common than all violence against Muslims, but he is rare in this respect.) Individuals who openly criticize and comment on the discrimination, both legal and systemic of religious minorities are given death threats and told to their faces that they are lying. Politicians who try to make laws that are more equal or less biased have been assassinated (especially in Pakistan). Non-Muslims are forced to apologize for "inciting" any rage that is manifested towards them. In a society where the discriminated cannot get their message into the open, people will not be able to realize what is happening.
4) Fifth Column: Jews, especially, but also Christians and Hindus are seen by many Muslims as fifth columns in Islamic countries supporting foreign powers. Jews are usually accused of being "Zionists", a term which is never properly defined, and supporting Israel. Christians are usually seen as supporting the West against the Islamic countries. Hindus are often seen as spies from India against Pakistan. This makes these minorities untrustworthy to the Muslim-majority unless they clearly disavow any association with the country/ies to which they supposedly have allegiance instead of the Islamic State.
5) Different Understandings of Speech Freedoms:Many Muslims, even in the West, believe that the freedom of speech ends where their offense begins. There are blasphemy laws in over half of the Islamic countries around the world. This is in contrast to the Western definition where many forms of even hateful speech are protected. Muslims, especially in less developed areas like Afghanistan believe that they have a right to manifest violence in response to speech that they find offensive.
6) Conversion: Since apostasy is a crime in Islam and most Muslims cannot imagine why anyone would ever convert from Islam, there are a number of thugs that target apostates for death in several areas. On some occasions these anti-apostate thugs will target the Church or Temple of the religion where the apostate goes in order to "punish" that religious group for "soliciting" the apostate (as if the apostate was hoodwinked into joining that religious group as opposed to choosing it for himself).
6) Islamic Supremacism: Islam has several doctrines which are followed by a small radicalized minority that call for a continued conquest of Non-Islamic Countries to be ruled by Muslims and to become part of a worldwide Islamic Empire. These groups believe in using violence to as well as politics to overpower and frighten Non-Muslims into accepting their school of thinking.
