I've also been reflecting further on the reasons why I care so much about the business models of GitHub and Atlassian in particular, but am comparatively unconcerned about the business models of other proprietary services I use (like Gmail, Feedly, Xero, ShareSight, Dropbox, or ThoughtStreams itself).
I think it mostly has to do with the role both companies now play in introducing many people to the idea of open collaboration (through GitHub and BitBucket respectively). No matter how much either company says they support open source, their actions say that they fundamentally believe the notion "You can't make money writing open source software".
There's no other way to rationalise their actions - GitHub have even stated explicitly they will never open source the core Rails application. If you'd love to see a cool new feature on GitHub, you can't send them a pull request for it - you have to hope that someone in the blessed inner circle with access to the source code will offer.
Atlassian have exactly the same problem with BitBucket - BB 2184 (adding CNAME support like that offered by GitHub Pages) likely would have been added long ago if they accepted external contributions. As it is, the lack of that feature is the only reason I have any repos on GitHub - the site publication repo for Curious Efficiency lives there.