How do I defend naval units from city defenses?

I'm in the late game and my aircraft carrier was one shot by a city defense (many of my information era units are destroyed in one shot). I'm going for domination and it's very hard to reach my opponent's capital in the center of a large continent. I've built up an airforce and am slowly making progress, but I'm wondering is there something I can do to counter strong city defenses and protect my units?