A lot of the Onion pieces are written at two levels. That's why I said it may not be for everybody because not everybody enjoys or gets that kind of humor.
When the Onion writes the pieces that make fun of Christians, a lot of Christians don't even get that they are being made fun of. They think the Onion is making fun of God. Which at the obvious level it is. But that's not the point of the piece.
The point of the "Very Special Forces" piece was not to make fun of disabled people. It's true that the piece did do that. But that was not who they were ultimately making fun of. I guess you can argue whether it's okay to make fun of God or disabled kids as a means of making a more subtle jab at someone else (politicians, Christians, etc.) But most people who read the Onion once don't even realize that there is a second, more subtle humor present that is the actual point of the piece. That's pretty much the reaction I see to every Onion piece, be it perceived as making fun of God, disabled kids, or someone else.
I can understand someone saying that it's still inappropriate even after they understand what's going on. But a lot of people perceive the Onion as being out to be cruel, hateful, blasphemous, etc., just for the sake of cruelty, hate, blasphemy, and that's where I think they are wrong.