It is a creative twist on a saying. The saying is "Time flies." It means "Time seems to go quickly."
(It is a very old saying--it is actually a translation of a Latin proverb, "Tempus fugit.")
"Time flies" is often used fatalistically. Time just flies past and you can't slow it down.
The saying twists "flies" to have a double meaning. An airplane flies, and an airplane has a pilot who guides and controls it. The saying means that even though you cannot slow the passage of time, you are in control of how well you use the time you have.
It is the same sentiment expressed in Rudyard Kipling's poem "If--," when he writes
"If you can fill the unforgiving minute
With sixty seconds worth of distance run..."
The saying also is a creative twist the pattern of family of jokes, so-called "Good news--Bad news jokes," which are usually pessimistic and slightly nasty--the joke is that what sounds like good news is really bad news.