But it might be worth noting that you can use spread-spectrum techniques (http://en.wikipedia.org/wiki/Spread_spectrum) to overcome jamming. Spread spectrum has some similarities to an encryption scheme, because the method used to smear the signal around uses a pseudorandom sequence which is known to the encoder and the decoder.
CDMA (http://en.wikipedia.org/wiki/Code_division_multiple_access) cell phones use this idea.
As you note, this type of encryption takes place at the RF level.
You increase your timing accuracy by 10x, and the jammer's power requirements increase by 10x (crudely speaking -- not a 1:1 trade, but directly linked).
We're talking about direct sequence, which increases the bandwidth of the signal but keeps the same carrier. To jam that (theoretically) you need large power through the entire band.
Both frequency-hopping and direct-sequence spread energy over a larger bandwidth. Direct-sequence does not explicitly frequency-hop, but the time-domain switching it uses will spread the energy out in Fourier space.
http://en.wikipedia.org/wiki/Direct-sequence_spread_spectrum
DS Spread Spectrum spreads the signal over a larger frequency range- because power is conserved it can even hide behind ambient noise.
When un-spread, the noise is spread out and the signal is "collapsed" back to the original bandwidth.
The most basic of jamming is to drown out all other communications with high-power noise. But in the case of illegal/covert activities this isn't ideal as your transmitter will be pretty easy to find.
So then you have to pretend to look like a legitimate signal. Which is where encryption and modulation can help. But then application level encryption isn't going to help against basic jamming.