True, maybe having your code in the open is overrated. I have to admit that I'm not talking from experience when I say it gives an edge.
Still, as part of a 2-minute research on a candidate, having LinkedIn and Github appearing first, instead of, say, a World Of Warcraft forum and your MySpace page, most likely help. (Not saying that this is necessarily fair, though.)
Maybe some companies like the idea of you having a Github account (maps to "really into coding" on their candidate checklist) but don't have the time to actually evaluate the code that you've posted, due to having too many candidates/applications to sift through, etc. That could be one explanation...