You can hardly blame them for being outraged as all hell...anti-Semitism runs very deep in Islamic doctrine (also in Christian doctrine, but western Christians tend to ignore this).
I haven't read the entire Quran, but the selection that I have doesn't really seem anti-semitic any more than any other religion would be. Take for example the following selections:
Quran said:
Many of the People of the Book wish they might restore you as unbelievers, after you have believed, in the jealousy of their souls, after the truth has become clear to them; yet do you pardon and be forgiving, till God brings His command
The opening of this section indicates that there is already conflict between Islam and the other Abrahamic Religions (including Judaism and Christianity). Yet it advises them to be forgiving, and to leave that judgment to God.
Take also into account that the first converts to Christianity WERE Jews. In the Acts of the Apostles, in Peter's sermon to the Jews while he does talk about how they handed Jesus over for crucifixion his response to then was that they could seek forgiveness:
Acts of the Apostles said:
For the promise is to you and to your children, and to all that are far off, whomsoever the Lord our God shall call.
It is also a teaching of the Church, that the crucifixion was to carry the burden of the sins of ALL peoples, across all time... not just those of the Jews. As for anti-semitism, the Church has made efforts to make a stronger connection between itself and the Jews, just recently I read about them changing the language of a prayer in order to be less offensive to the Jews.
Nonetheless, despite this message of forgiveness tension between cultures arose in the Medieval period. I will again emphasize that despite embracing the religion, the barbarians that took over after Rome's fall were very warlike and so their political culture of war tried to draw religion into it. It was not the religion that dictated this conflict, it was the inability of these two peoples to get along and so they started to use religion as a way to fuel these tensions.
This is the state of affairs when Mohammed comes onto the scene, with his own interpretation of the Abrahamic faith to spread but now his religion is just another part of the already existing conflict.
Quran said:
The Jews say "The Christians stand not on anything"; The Christians say, "The Jews stand not on anything"; yet they recite the Book. So too the ignorant say the like of them. God shall decide between them on the Day of Resurrection touching their differences. And who does greater evil than he who bars God's places of worship, so that His Name be not rehearsed in them, and strikes to destroy them?
Once again, we see a "God will decide" thrown in, as an answer to the conflict between the Christians and Jews. I included the last part because while its very likely this is in response to attacks on Islamic places of worship, since Jews, Christians, and Muslims worship the same God, this statement should discourage also attacks on synagogues and churches. While Islam considers them unbelievers, the Quran plainly states they believe in the same God:
Quran said:
And they say, "Be Jews or Christians and you shall be guided." Say thou: "Nay, rather the creed of Abraham, a man of pure faith; he was no idolater." Say you: "We believe in God, and in that which has been sent down on us and sent down on Abraham, Ishmael, Isaac and Jacob, and the Tribes, and that which was given to Moses and Jesus and the Prophets, of their Lord; we make no division between any of them, and to Him we surrender."
If all three religions worship the same God, why is there such conflict? The religions should all be able to have peaceful conflicts. They can argue over doctrine, and plead common ground on the doctrine they share. Oh, there's this part, I believe this is that tricky part you've been talking about:
Quran said:
And fight in the way of God with those who fight with you, but aggress not: God loves not the aggressors. And slay them wherever you come upon them, and expel them from where they expelled you; persecution is more grievous than slaying.
...but if they give over, surely God is All-forgiving, All-compassionate. Fight them, till there is no persecution and the religion is God's; then if they give over there shall be no enmity save for evildoers.
...holy things demand retaliation. Whoso commits aggression against you, do you commit aggression against him like as he committed against you; and fear you God, and know that God is with the godfearing.
(emphasis added)
Its somewhat a problematic passage, looking at just the words used it appears to contradict itself between the first and the third selection I included. However, looking at the meaning behind this passage, I think its very important to pay attention to the part that I italicized. It advises quite ruthless behavior, but it is only for
retaliation. In other words, a dramatic example of eye for an eye. The middle selection still speaks of forgiveness.
It is also important to take this into context. Islam was born in the middle of warlike Arabia, and the pagan Arab tribes made it very difficult for Mohammed to get a foothold there so after his exile he came back and fought them. This is why he advises retaliation. Earlier in the passage, where it said that there is no greater evil than preventing worship of God is probably the tenet of their faith that justifies going to such measures. When have we ever shown such desperation? World War II comes to mind...
However, as with most holy texts, the way its interpreted means more than the what is actually set in there. Much of the conflict between Protestantism and Catholicism is over the interpretation of the Bible (individual versus centralized interpretation). The way that the Quran is interpreted would be different depending on the culture that interprets it.
This is a pattern we saw in the Middle Ages with Christianity, where because Christianity was professed by a warlike people, they interpreted it in a warlike manner at which point they became the aggressors that the Muslims were advised. If it fits the political agenda of whoever is in charge, they could claim that we are the aggressors for meddling in the Arab world, for getting involved in conflicts in Israel, Afghanistan, and Iraq. Of course, that contradicts this passage, directly following the eye for an eye bit above.
I repeat again, the middle-east has been a hotbed of political conflict for centuries. Protestants interpret the Bible in any way they please, and most of the time they interpret it as a message of forgiveness and peace. Our political culture, especially pacifist sentiments of the people in response to the cold war, allows us to see other interpretations as radical. It is for that same reason why I, as a student in America, would interpret the Quran differently than another citizen who is looking for something to blame for terrorist's attacks on our country, or than someone in the middle-east. For what I see as an "eye for an eye" passage aimed to defend their right to hold their faith, the other two may see as a call to war.
You say that it is easy to use religion to justify pretty much anything, but why would they use religion? For political reasons. I do want to note that you said "modern political tension" and I would say that in the case of the middle-east, its not completely modern. A lot of growth has been prevented because of continued political tension from early times. (There was a time when this was reversed: again, the Medieval period)
I do not subscribe to the Islamic faith, but I am unwilling to demonize another religion or the people of that religion just because of the current media. I believe that conflict between religions should be peaceful debate over doctrine, and should not be drawn into wars which only end in shame.