The only feasible means of protecting America's homeland from foreign terrorist attack is to eliminate all terrorist-supporting states. We opposed some foreign terrorism before 9/11, but weren't at "war" with terrorism in general. 9/11 forced us to recognize that most foreign terrorists and their state sponsors cooperate to a greater or lesser degree, and that our security requires rooting out what has grown into a connected system of world terrorism and the state sponsors of its disparate parts.
President Bush indicated in a recent speech that all governments which continue to use terrorism as instruments of state policy, if only to deflect their own people's anger away from themselves towards us, will be forcibly replaced. He did not, however, mention what will happen when replacing a government won't improve the situation, which will usually be the case with failed/failing states.
Their fate will be extinction. I.e., failed and failing states which have served as terrorist sanctuaries will be conquered and occupied by a friendly country (us if necessary) with the means and ruthlessness to root out terrorist infrastructure.
This is a fundamental change in the post World War II order. Borders will change and whole countries cease to exist. The world will be rearranged to further our domestic security, and we will act preemptively rather than waiting for attack. These are logical and necessary implications of America's new policy, i.e., we'll get there eventually despite claiming the contrary now.
It's a bit hard in places to tell which parts are descriptive of the Bush strategy and which are prescriptive, but it's all worth reading. This article on terrorist radiological weapons is also useful and troubling.