Tony Morrison's "Song of Solomon" which is classified in the genre of Magical Realism ends her novel with the image of flight: Milkman, who has finally found his family roots leaps into "the killing arms of his brother [Guitar]" who has followed him in the hope of finding gold that he suspects Milkman of hiding. Throughout this novel the motif of flight/escape is present as the novel begins with Robert Smith's attempt to fly off the top of a business building, to Pilate's being able to "fly without leaving the ground."
Flight as escape is certainly the main theme of John Updike's "Rabbit, Run" in which the main character, Henry "Rabbit" Angstrom, frustrated with his life, jumps in his car and drives and drives after having left his son in the care of his in-laws. In his flight, Harry seeks something that will give meaning to his life.
There are lots of these. A few that come immediately to mind are--Lord of the Flies (the boys are put on a plane to escape the horrors of war only to encounter the horrors of barbarism and the dark side of humanity), The Catcher in the Rye (Holden runs away to escape his situation only to discover that there is some kind of trouble everywhere and that lots of people are "fakes"), Frankenstein (Victor runs away from his creation in the hopes that it will "go away" but he discovers that a problem not dealt with only grows in intensity to the point that everyone Victor loves loses his or her life). These are not examples of literal "flight", but I think that a figurative "flight"--ie running away--would also count for your question. Good Luck!
The story that comes immediately to mind is John Steinbeck's story that is called "Flight." In it, Pepe is drawn by fate and circumstances into killing a man. Pepe is poor, uneducated, and powerless. As a result of his situation, his only course of action is to run, to flee into the nearby mountains to escape those who will surely pursue him and kill him. In the story, those who pursue Pepe are called "the dark watchers." Despite his efforts, Pepe cannot escape. He dies, suffering and alone.
Another, more subtle example of flight as representing escape and freedom can be found in A Separate Peace by John Knowles. The novel is set at Devon, a prep school in New Hampshire, during World War II. In that novel, the main character, Gene, has betrayed his best friend Finny and suffers from guilt and fear, as a result. Gene's emotional turmoil becomes so great at one point in the novel that he decides to enlist in the military. Gene sees going to war as a means to escape being trapped by the past, and he believes that leaving Devon behind will bring him freedom and relief from his punishing emotions. As it happens in the story, he does not leave, however.