A CNN article estimates that fewer than one percent of flights are protected by air marshals. Though the Transportation Security Administration doesn't make public the number of flights air marshals cover, a number this low suggests there's a breakdown in the system somewhere.
CNN did its own investigation for this story and spoke with a number of pilots and current and former air marshals—all of whom remained anonymous. Pilots report that they've been seeing fewer marshals aboard flights, and marshals themselves say the American public would be shocked by how few air marshals are flying. They also question where the budget is going when the number of marshals is dropping.
The story includes a response by the federal air marshal program, which basically says there's nothing to worry about. But it rings hollow in the context of the story.
This news won't do much to help you feel safer while flying, but the hope seems to be that drawing attention to the problem may bring about a speedier solution.