Yes there are a few reasons for that. Mostly cost (it runs on 2 servers) and it can only index things that are publicly exposed. Since the majority of code released is in github it tends to skew towards it as the main source.
It does however index the following (and more) repository locations, Github, Bitbucket, Fedora Project, Google Code, CodePlex, Sourceforge, Tizen Project, Google Android, Minix3, Seek Quarry, Gitorious and a collection of sources from GNU Savannah.
Im always looking to add more, so if you know of say a github for fossil projects (tarpit would be an excellent name for this BTW) let me know so I can add and index them.
the debian code search, on the other hand, has access to all software shipped with debian: https://codesearch.debian.net/
this is arguably another silo, but the diversity of software in there is also interesting.