We're all businessmen here and everybody knows I hold absolutely no ill will towards Github for what I am about to say, right?
The primary concern was what SEOs call link equity (a link to your site from a trusted domain is a signal of trust, Google uses trust as a signal of quality in determining rankings, rankings are worth money, thus inbound links are essentially illiquid capital), with brand recognition being a major secondary concern. Take a look at Rails blogs discussing the OSS packages they use: everybody cites the canonical version of the code and if that is on Github then they cite the page on Github, frequently to the exclusion of the author's post or page about it.
Related problem: Frequently authors don't have a substantive page about it. That would be a mistake if you're trying for link equity or personal branding, in my mind. Relatedly, I spent $250 on a logo.
I spent quite a bit of time on that project and wanted the various marketing benefits of it to accrue to me, not to Github. So I put it on my site, not theirs. Folks subsequently cloned the repository and put it in their Github accounts. I am totally OK with that: mine is the canonical one and the canonical one gets the links, mindshare, etc.
This is the problem I tried to solved with the Indefero hosting I offer. All the forges have their own domain name for free and you can migrate all your data to your own server with your own Indefero installation in 3 easy steps (download, import, switch DNS).
Anyway, the problems with Github is that their level of quality result in people considering all the offers as having such level of quality. We (code hosting providers) are all suffering when Github is down... this is where it annoys me.
