The initial post has omitted any reason for the change. Of course people would speculate, including in the HN comments.
What seemed majority at the time was the idea of some collaboration/partnership and monetary exchange.
I think its a good lesson in communication, especially when you have a dedicated community. Transparency is welcome.
Regarding Atari and "their rights", there hasn't been an Atari for way too long and the IP was passed between companies left and right without additive value to users. I expect transport tycoon to be another cash grab, but happy to be surprised for the better.
Atari being the commercial firm it is, I could very well imagine that stuff was under NDA. Just 'by default', because that's what the lawyers like. And only when angry speculations emerged they could be persuaded to just openly communicate.
Or the OpenTTD guys were not the best communicators. Considering it's the OpenTTD creators live at the intersection of the groups 'programmers' and 'adults who like to play with train sets' it wouldn't be a stretch.
All in all I think this collaborative approach is very much the preferred outcome.
All those people saying 'the open web is dead' and 'people don't download from websites anymore' are exaggerating imo.