Why?

First, the families of U93 victims support the movie. Here. Here.

Second, 10% of the profits were being donated to a memorial fund. Again, with full support of the families.

Third... there's the argument that it's so. horribly. wrong. to benefit financially from a movie about such a tragedy.

Really.

Have you watched:

Schindler's List
Saving Private Ryan
Fahrenheit 9/11 (which, oh, by the way, made $204,114,517.00 and Moore did not donate any proceeds to charity, the company he sold the rights to did, though)
Bowling for Columbine
Pearl Harbor
Titanic

No one makes movies in Hollywood just for the joy of making movies. They do it for profit. If we relied on people making movies for the sake of charity... many important stories would never be told.