As USAF MD'05 pointed out, it's very easy to apply to two different specialties.
When you download the JSGMESB application in late summer, you have two separate forms to rank a primary specialty and a second choice. For either, you rank deferred and any AF base offering your specialty.
There is a second choice form where you can rank another specialty and rank order your choice of base/deferrment. It is VERY dangerous to rank a non-competitive specialty as your second choice, especially if you're going for something competitive in the military (i.e. EM, rads, even ob/gyn).
"It is not mandatory to list a second choice. Applicants should make sure they will be equally as happy in a second choice of specialties as they would be in their first choice before completing this form. Remember, all board decisions are final and if selected for the second choice, individuals may not decline training after the selection board. If selected for a full residency, individuals most complete a minimum of one year of traning the selected specialty."
You can choose not to fill out the second choice form, either, which I highly recommend if your first choice is your dream field. I ranked a second choice, but it was neurosurgery so I figured I had a snowball's chance of getting that.
As others have noted, you may want a particular specialty (say Ob/Gyn) and still get hosed based on your second choice. You may do Ob/Gyn rotations at every base, get letters of recommendation from all Ob/Gyns, etc. You may send your application only to Ob/Gyn military programs. If you put family medicine as a second option, you're stilly in serious danger of being an FP. It happened to a good, highly competent friend of mine who even had prior military experience.
If you want to a flight surgeon, don't even worry about this stuff, tell them you only want a one year training slot as your first choice. They even state that on the form.