The Sunnis had empire. They lost it.
They had privilege. They lost it.
The Sunnis treated the Shi'a badly. Then, when the Shi'ites got control, they returned the favor. Which really grates against the Sunnis' sense of entitlement--they properly had control and dominance and privilege. Now they're humiliated and in some societies, humiliation is grounds for a blood feud and is often perceived at a clan or tribe level.
But that's not all of it. Saddam played up the situation and made matters much worse in the '80s. The Sunnis went from being very educated and secular to very much retrograde under Saddam. The Iran-Iraq war was sectarian; the Shi'ites and Kurds were unreliable cannon-fodder, and it was the Sunnis that were the heart of the country. Religion was highlighted, mosques that had never been Sunni were "reverted" to Sunni control. Traditional Sunni tribal structures, which had lost influence during the secularization and modernization campaigns of the '60s and '70s, suddenly had their influence restored and funding sharply increased. Even in Baghdad tribal affiliation became important, with important tribes and lesser tribes (and then the undertribe of the Shi'ites). In this, he took a page from one of his heroes, Stalin: Anti-religion and internationalist when it suited him, when Hitler attacked suddenly the seminaries were re-opened, churches were okay (at least the Russian Orthodox Church), and it was rah-rah Rah-ssiya! Or at least "rah-rah Russians". So while Ukraine lost more men to Hitler, both civilians and soldiers killed than Russia did the victory was clearly a Russian one. So while the Shi'ites had more civilians and soldiers killed than the Sunni did, the victory was clearly a Sunni one. The Ukrainians and Shi'ites were both still untrustworthy.
By 2002 a large number of boys were functionally illiterate. The school system was a wreck, underfunded during the war with Iran and never refunded. Girls seldom went to school, both because of fundamentalism and because of capacity shortfalls. The elite Sunnis were not just Sunni--they were rich and loyal to Saddam. The situation Cole describes was short-term. By 2003 there was a clear bulge in Cole's educated Sunni population. If you were under 20, you probably weren't well educated. If you were over 50, you probably weren't well educated. If you were educated from 1960 to 1985, you got a good education. Esp. if you were Sunni. (Sort of apartheid-like, don't you think?)
This official return to a kind of fundamentalism served Saddam well in the '80s. Anti-Western hysteria served him well in the '90s. But in the '00s he found that the fundamentalism was at risk of being subverted by "better" Sunnis than he was, even with his grand mosque with Scud-missile-shaped minarets and blood-inked Qur'aan. If Saddam hadn't embarked on his use of religion as a political tool, who knows how the Sunnis would have seen themselves by now. Probably more like Kurds see themselves, for all their flaws. And it wouldn't have further galvanized the Shi'ites to do the usual thing, to go from oppressed to oppressor and justify their oppressing others as "historical justice." (A phrase that has become more odious as I've grown older and seen it for what it is--an excuse for people today to oppress the living in the name of the dead, many of whom would denounce their descendants.)