Does the Qur’an Teach Hostility Against Non-Muslims?

Dear Scholars,Assalamu ?alaykum,The Jews and Christians are called kufaar in the Holy Qur?an because of some of their beliefs and actions. However, the way some scholars and writers frequently use the word nowadays connotes hatred, hostility and killing of innocent Christians. In some countries, whenever there is a misunderstanding between Muslims and Christians, Christians will be killed and there churches will be burnt or destroyed and the Christians usually retaliate inflicting higher casualty on the Muslims.Some of us think that we Muslims should respect the places of worship of the Jews and the Christians and their life even though they are kufaar. Some people have called our attention to some comments of some of our respected Scholars; for example:1. Sheikh Ibn Taimiyah was reported to have said: "[The following is] a disbeliever: Whoever believes that churches are the houses of Allah in which He is worshipped or who thinks that what the Jews and Christians do are valid acts of worship of Allah and obedience to Him and His Messenger, or loves or approves of what they do, or aids them in having such places and establishing their religion, and he does so thinking that is a way of getting closer to Allah or worshipping Allah."But we read in the Holy Qur?an: "(They are) those who have been expelled from their homes in defiance of right (for no cause) except that they say "Our Lord is Allah. "Did not Allah check one set of people by means of another there would surely have been pulled down monasteries churches synagogues and mosques in which the name of Allah is commemorated in abundant measure. Allah will certainly aid those who aid His (cause); for verily Allah is Full of Strength Exalted in Might (Able to enforce His Will)" Q22:40.Some of us think that ?Whoever believes that churches are the houses of Allah in which He is worshipped? may be responsible for the burning and destruction of Churches whenever there are misunderstanding between Muslims and Christians in some countries.Are there any instances in the past (during the time of the salaf) when Muslims destroyed the places of worship of the Jews and Christians when they conquered their lands? Please explain the meaning of the statement in relation to the verse.2. Some Muslims think fighting and killing non-Muslims is allowed because Allah says: ?Fight those who do not believe in Allah or in the Last Day and who do not consider unlawful what Allah and His Messenger have made unlawful and who do not adopt the religion of truth [i.e. Islam] from those who were given the Scripture ? [fight] until they give the jizyah willingly while they are humbled.? Q9:29.What should be our understanding of the above verse now that the Muslim countries are weak and Islam has spread all over the world and Muslims are the minority in many Non-Muslim countries? Are Al-Qaeda members and their supporters following verse Q9:29? Is there any Muslim country nowadays where jizyah is collected from non-Muslims? If no, why?May Allah reward you abundantly for your answers.