The 'free' air is usually from certain major airports and those outside of those airports will pay an extra premium. Plus, often these airfare promotions have routings that you may not like.
However, keep in mind that those 'free' airfares aren't really free. As your mother always told you, if it sounds too good to be true, it usually is. The funny thing is that if you ask them how much the cruise is without the 'free' airfare, the cruise fare is less. Wait a minute; if the airfare is 'free', then how can the cruise be cheaper if you decide you don't want the 'free' airfare???
It's one of those little 'tricks' they like to play on people who aren't savvy on the matter and are booking it themselves directly through the cruise line, so they don't think to ask alot of questions.
Most of the time, we find when we book our clients without the 'free' airfare and then do the air independently, they usually pay less and get a much better routing.
It's always good to let your agent do some research to insure you're getting the best possible deal for you.