I would not eat the price of the airline ticket. Through nobody's fault, there was a rain delay and plans were already made. Travel ball teams are put together in the fall and players make commitments to the team when they join. Conversely, I would not hesitate to cut a player who missed the PGF qualifiers.
You have to be an idiot to put yourself in the position of missing the flight due to a rain delay. The expectation that the game will finish on time and you can make an evening flight later in the day is unreasonable.