Here's a question for the techno-libertarians stepping up to say the government has no right to shut down sites like Silk Road. Where do you derive this supposed natural right for anonymity on the internet? Life, liberty, freedom from discrimination, due process--these things I understand, and there are well supported philosophical frameworks (rule utilitarian, Kantian, libertarian etc.) for deriving them from first principles. I can also understand a society guaranteeing a right to privacy in limited circumstances: crimes affecting children are one obvious example, records of education and medical treatment are another. In each such situation, the benefits, harms and impact on the rights of the public and the individual have been weighed.
But an anonymous free-for-all exchange being a natural right? We aren't born anonymous. In the "state of nature," without government, we are in no way anonymous. The fact that the internet sometimes allows us to be is in fact a very artificial circumstance that society has allowed to happen. Whether we like it or not, governments are ultimately the overseers that permit networking infrastructure comprising the internet to be built. That isn't some natural right any more than building a nuclear weapon in my backyard is a natural right. Society has weighed the pros and cons and decided that this particular set of technologies is on the whole good. That it might in fact want to limit the level of anonymity on the network seems reasonable, in the same way that making people put license plates on their cars is reasonable.
I'm not supporting the idea of a government ID to access the internet (although some first-world countries already require some level of this), or nationwide surveillance a la China or the NSA. Anonymity no doubt has societal benefit, in that it has fostered great works of creativity (from Mark Twain down through Anonymous). Unfortunately, society depends on accountability, and accountability and anonymity are competing principles in the construction of a just society. Neither of them are natural rights on their own.