PZ Myers is, of course, a God to whom we must all Bow Down and Worship. But he's not always right. He makes a fundamental mistake in his evaluation of Digg. The problem is not with the "Digg Patriots"; the problem is with the premise of Digg itself, or, rather, with how one takes Digg. Digg is a method to discover web sites and works that are uncontroversially popular, in much the same sense that Wikipedia exists to document (relatively) uncontroversial knowledge. Anyone who uses Digg or Wikipedia to find important or authoritative information on socially controversial topics — whether that controversy does or does not relate to any objective or scientific controversy — is using a hammer to drive a screw.
Not that I in any way approve of their positions, but the Digg Patriots are exercising their freedom of speech; they are in no way limiting or compromising freedom of speech. They are using one specific private system of measurement, a private system that has no responsibilities at all except to its creators, to express their opinion, specifically their opinion that Pharyngula sucks.
I don't think Myers' suggested strategy — that admirers of Pharyngula and other pro-science, pro-skepticism and liberal sites vote those sites up — will be effective. Digg exists to highlight uncontroversially popular sites; there's little difference in the Digg universe between (apparently) uncontroversially unpopular sites and controversially popular sites.
Vox Populi is nothing more or less than just Vox Populi; the Voice of the People is neither the Voice of God nor the Voice of Satan. If you want to be popular, snark on celebrities or put funny captions on pictures of cats. If you want to talk about the truth, don't expect to be popular, and especially don't expect to be uncontroversial, and don't be all butthurt when you're not.