Most flights do not have air marshals, according to an August 2014 report in USA Today. This article and a CNN report from February 2014 estimate that there are some 3,000 marshals and that of these, many are working on the ground.
John Casaretti, National President of the Air Marshal Association/CWA, says in the USA Today report that with 30,000 daily commercial flights in the U.S., placing two air marshals on each would necessitate a work force of more than 75,000 marshals. As a result, marshals board only a tiny portion of flights. A computer program chooses the flights for marshals to board based on threat probabilities, the amount of fuel on the plane and other factors.