So Github gives their product away to people that don't have enough money to host on their own secure servers, and... what else? Where do they make their money? It seems from the comments here that their enterprise market is trivial.
As a business strategy, Enterprise software has plenty of room for a profit margin. As it stands, they have mindshare and are probably actually breaking even, or making at least a modest profit. This funding round is probably more about flushing out their enterprise offerings, so they are better in terms of competing with alternatives, or even bringing in better bridge/migration support.
I've seen/used Jira, TFS, SVN and plenty of other systems that integrate project management and source control. There's definitely room for much better tooling here, and Github is in a better position than most to take over this space.