The Latics had an opportunity to climb out of the relegation zone by winning the game they had in hand on their fellow strugglers on Tuesday night, but they went to a 3-2 home defeat.
The result leaves Wigan three points from safety with just two games of the season remaining, but chairman Whelan was in philosophical mood after the final whistle.
"Sometimes you play very well, sometimes you are average and sometimes you are poor, and I think we fell into the class of playing very, very badly," he told Sky Sports News.
"The lads will all realise that, Roberto (Martinez) will know, and the crowd was seriously disappointed.
"The game was there for the taking, but in football you have to take the rough with the smooth."
Wigan's next league game is away to Arsenal next Tuesday but they must first take on Manchester City in the final of the FA Cup on Saturday.
While Whelan would love to claim some silverware, he admits that if he had to choose he would prefer to stay in the league rather than win the FA Cup.
He said: "We've got to take survival, but the cup is a very, very good secondary trophy.
"The FA Cup is the FA Cup, but survival is what it is all about."