I find it informative to compare Silver's projections with the Real Clear Politics averages. RCP is a group project, but it's pretty clear that their editorial views skew heavily toward the conservative end of the spectrum. Assuming either is biased, I figure that Obama can't be doing any worse than RCP is projecting or much better than FiveThirtyEight.
Your link just says because Nate Silver talks about Obama in his blog the site is a propaganda tool. People don't visit for the blog, they visit for the numbers and research. Personally I think it would be the other way around, if he were also a popular Obama blogger but did FiveThirtyEight anonymously that could be considered sinister (it still wouldn't be unless the model was proven wrong, but there would be a perception of deception).
I've seen him a couple times on HDNET and he's extremely clever. I'll be watching him tonight instead of the hacks they put up on the major networks.