Just invest in more bombers than they do... works every time :-)
Alternatively, you can invest in air defense units. You can only have a handful (6 i believe) per area, but they are a lot easier to get than boombers. I just make sure to have at least one built as soon as the nuclear epoch approaches.
The anti-aircraft units are also a good investment, but they're pretty expensive. They are amazing.. not only because they seem to have a higher hit rate, but they can be moved around (unlike air defense).