A salutation of well-wishing.
Originally Pilots' jargon, now widespread in use.
Active RADAR systems send out a radio signal which travels to infinity in most cases. When the beam hits an object, however, it is reflected back to the transmitter, where the signal can be used to indicate the presence of an object (e.g. an airplane). However, when the radio waves are emitted at an angle such that they skim close to the ground, there are small reflections from trees, rocks, buildings, mountains and other land-based objects. These constructive and destructive reflections creates a great deal of interference or noise in the receiving RADAR antenna.
By keeping an airplane travelling at low altitudes (particularly stealth aircraft), a pilot can keep the recognizable RADAR signature of his or her plane well within the noise of other reflected radio waves. This masks the airplane's presence from the RADAR station.
In general, this is a Good Thingtm as RADAR stations typically are connected to launch systems for surface-to-air missles. By hiding oneself, one keeps those missles not operated by one's allies from being launched at one's plane.
Thus, when originally using the phrase "Fly low and beat the RADAR," it expressed a hope for the other person to have a safe flight and mission. It has come to be a general wishing of "good luck" or "good fortune."