1. ...He always counters that groups in the Middle East have Always hated us, and that they would try attacking us no matter what.
First, acknowledge that your father may be a lost cause. That doesn't mean you have to give up, but face it: the guy is hardwired into the propaganda machine (Limpboy, Manatee, O'Biley), he loves YOU, but he respects them a whole lot more (he didn't change their diapers). So, don't fixate on unplugging your father. Be prepared to move on.
Having said that, ask the genius why he believes America is the #1 target of "the terrorists."
Is it because we aren't a muslim country? If that's the motivation, why not Russia, China, Ireland, or Switzerland?
Ask him if he believed Dubya's claim that "the terrorists attack us because we're rich and free." If that's their motivation, then ask him to create or find a comparative chart of countries ranked according to their prosperity and civil liberties. If Dubya was right, then other prosperous and free countries ought to be experiencing attacks by muslims in proportion to their relative wealth and freedom.
When all else fails (and it will), ask him how he'd feel if he came home from work next Wednesday, and found a bomb had been dropped on his neighborhood and his family had been killed. Ask him whether, when he discovered that the bomb said "made in China," he would passively accept that his home and family had the bad manners to place themselves between China and her belief that her national security interests depended on a demonstration of international military strength. Would your father turn the other cheek, or would he go Old Testament until those God-less Chinese wished they knew what the Golden Rule was?
Then, ask him if maybe -- just maybe -- it's possible that one tiny fraction of the motivation for the terrorists hating our guts (aside from our wealth, freedom, and religion, of course) is that of the hundreds of thousands of faceless men, women, and children that have been killed with our bombs (or with the ruthless, robbing, raping, and murdering dictators our politicians have propped up) a few of them had loved ones who survived them, loved ones who found bomb fragments that said "made in America."
Ask your father if there is even the remotest possibility that his beloved son is right about any of this. If he says "yes," your seed has taken root. If he says "no" ....if he says "no" ...then you just may have to face the possibility that your christian father, like millions of other Americans, has been irreparably neoconned.