Wigan lost striker Emile Heskey to a suspected broken metatarsal early on and boss Chris Hutchings admitted his side were second best for long periods.
Fulham boss Lawrie Sanchez said: "I would have thought that was about as comprehensive as you can get without actually winning a match and ultimately we were hanging on.
"Last week Tottenham should have killed us off before we ever got back into the game and we got something we shouldn't have got and plenty of plaudits for it.
"This week we should have killed Wigan off. It was the most one-sided game you are ever likely to see in the Premier League, right up to the last 10 minutes.
"Then a penalty pretty much out of nothing and we were hanging on and Scharner should have scored to win the game. It just shows you should not leave early when we're involved.
"I'm disappointed. I think Chris will be happier. It's difficult when you've played so well away from home, especially when you're a team which doesn't win much on the road."