There are other reasons too, sometimes. Re-Volt, one of my most favorite games ever, used to be on GOG for a short while. If you've ever tried to play it on windows 7, you know that you either have to run it with a certain command on the .exe or with the unoffical 1.2 patch made by the game's fan community, which, by the way, still exists, and has no intention of going away.
An Asian company which acquired the rights to Re-Volt, decided to just upload the game with the fan-made patch without telling anyone about it. There was an outrage in the community and the joint effort of the leaders of that community lead to the game being taken down from GOG. I know that might seem selfish to a passerby but keep in mind that the company which bought the rights to the game has been continuously screwing with the piece of art that Re-Volt is.
There was a guy in the community who was working on an Android port of the game. He'd probably release it for free or for a really small price. And he would have done the job properly. Unfortunately the C.E.O. of WeGo Interactive (the company which now owns Re-Volt) wrote him an e-mail, in horrendously bad English, ordering him to stop.
He did, as he had no choice. Not much later WeGo released a crappy port for Android. Recently, they released Re-Volt 2. This is a total blasphemy and a bullet to the heart of every fan of the game. It's the same game, only the cars have different skins and you get different in-game purchases etc. It's downright insulting. (Keep in mind that a sequel to Re-Volt has been promised more than once by different companies, which had bought the rights to the game over the years, and none of them have fulfilled their promise. It's like George Lucas never made the prequels to Star Wars. Errr... maybe that's a bad example but you get the point.)
The moral of the story is that there are people who know very well that there is business to be made with old games, although the don't know how to conduct that business. They buy the rights, so GOG has a hard time dealing with them, and sometimes they just have to fold.