Something I think may distinguish the likes of GitHub and Atlassian from the traditional proprietary vendors that have given proprietary licensing such a bad name is the fact that even though their software is proprietary, it isn't a platform in the same sense that an operating system or a PaaS cloud service is a platform (in the case of PaaS, "platform" is right there in the acronym).
For those, customers really do need the full protection of open source licensing to avoid the kinds of abuse we have seen from vendors in the past.
Hosted services are a little different, especially with things like OpenShift Online becoming available to make self-hosting far simpler for many use cases. There, the customer base is generally more mobile, and while network effects do exist, they're nowhere near as strong as those that previously locked application developers and hardware manufacturers into dependencies on proprietary platforms.