Because unless it was placed into the public domain they still need permission to redistribute it. Ultima IV for the longest time was free, but only if you got it from one of a small number of specific web sites, if you downloaded it from anywhere else you were technically pirating it.
In the case of GOG, this is a commercial web site and using it as promotional material could easily run afoul of the owner's trademark.
Pretty much this. The thing about FOTAQ is that the rights were not with Renegade (and by way of inheritance, Atari), the rights remained with John Passfield, and he distributes the game on his website for free. He's allowed ScummVM to distribute it, but I'm not sure how he would feel about commercial exploitation of the property.