Not all maps include cruise missiles and the capture point required for cruise missile is usually the one in the middle of the map (often C). The maps that have cruise missiles usually have a large body of water bordering the map (for example Siege of Shanghai, Flood Zone and Hainan Resort). On maps where the cruise missile is unavailable, it is often (if not always) replaced with a gunship instead.
Added: You can see what commander assets are assigned to a point by highlighting the flag with your crosshair when not playing as commander. The little icon (if there is one) displays what commander assets is attributed to that point.