I know you're just trying to make a metaphorical comparison with railroads, but the story isn't that simple.
In the U.S., intercity railroads found they could make more money by focusing on freight and leaving passengers to poor Amtrak. If Warren Buffet's acquisition of BNSF is any indication, the private railroads are quite profitable.
The decline of intracity passenger rail in the U.S. has many causes (massive public investment in the Interstate highway system for one). Still, it's worth remembering that auto companies played an active role in acquiring and disassembling streetcar lines: http://en.wikipedia.org/wiki/General_Motors_streetcar_conspi...
And your comment reminded of something similar with Coke. At some point they decided that they weren't competing with other soda manufacturers but for "share of stomach" and started going in that direction by going on an acquisition spree.
Github doesn't have any central direction at all (people are more or less allowed to work on whatever they like), and this is a side-effect: the boring stuff doesn't get worked on, and the fun stuff (like, say, rendering 3d models, or a CLI in the header) gets lots of attention.
I think Github is probably vulnerable to a team that stays focused on the bread-and-butter tools that are actually important to developers.
I remember reading somewhere (probably here) that part of the reason the railroads failed to adapt to cars was because they thought of themselves as railroad companies instead of transportation companies. Maybe github is thinking of themselves as a collaborative work company rather than a collaborative coding company and trying to adapt to that.