You're spot on in your thinking.
I believe the "why" is mainly because the Qu'ran and other holy books contain many confusing and mixed messages, that are subect to interpretation just like the bible. Many of the versus don't attribute the vengance part to god but rather to the follower; this is a big difference from the bible IMHO, and an awful object lesson for any religion to teach.
It's passages like these below (there are hundreds more like it) coupled with zealous types (e.g. Muslim versions of elders and Pioneers) is going to continue to be used as tool to brainwash people, and create terrorists.
Quran (2:191-193) - "And slay them wherever ye find them, and drive them out of the places whence they drove you out, for persecution [of Muslims] is worse than slaughter [of non-believers]... but if they desist, then lo! Allah is forgiving and merciful. And fight them until persecution is no more, and religion is for Allah."
Quran (8:57) - "If thou comest on them in the war, deal with them so as to strike fear in those who are behind them, that haply they may remember."
Quran (9:14) - "Fight them, Allah will punish them by your hands and bring them to disgrace..."
Quran (9:123) - "O you who believe! fight those of the unbelievers who are near to you and let them find in you hardness."
Bukhari (52:220) - Allah's Apostle said... 'I have been made victorious with terror'
Bukhari (52:177) - Allah's Apostle said, "The Hour will not be established until you fight with the Jews, and the stone behind which a Jew will be hiding will say. "O Muslim! There is a Jew hiding behind me, so kill him."
[Related thread]