Real life isn't a videogame. It's very hard to hit a moving target. The Allies developed airborne radar, and could be on a surfaced u-boat before they could man the flak guns. The U-Flak boats proved to be a lesson in futility; all they did was tempt the crews to stay surfaced and die.
On our destroyer we conducted excercises against live aircraft. You have no idea how difficult it is.
http://www.uboat.net/history/aircraft_losses.htm
http://www.uboat.net/fates/losses/cause.htm