Call me crazy, but when was the last time we were worried about cruise missiles over DC? I realize that the US has less-than-perfect relations with some countries, but the Cold War has been over for quite some time now.
It depends on what you call a cruise missile. We are at the point where anyone can take off the shelf parts and software and make a "drone" [1]. It's a pretty simple matter to modify the software to order the drone to crash into a building, motorcade, or outdoor event. Making an effective payload that can be carried by your small aircraft is another matter.
Also, what's the point of defending only one city from cruise missiles? Unless the enemy has a specific political target, they can cause a lot of destruction elsewhere.
A missile hitting DC is likely more probable now that it was during the depths of the cold war. To another question poised by mapmeld, DC is of significant political and symbolic importance, not to mention the many military agencies involved in the same. A successful strike against the capital would be a huge morale boost for enemies, as 9/11 was.
I have to second what Second_Ender mentioned -- we are at a critical juncture where off-the-shelf components offer rather frightening possibilities. I love technology, but benign videos like http://www.youtube.com/watch?v=tMwSVDVJNWc&feature=youtu.be leave me deeply concerned about the future.
[1] - http://ardupilot.com/