This post is adapted from some homework I received at the University of Tokyo.
TL;DR: anonymity and encryption are two fights in the struggle between citizens and their governments. The best move for us is to fight fiercely and establish them as permanent rights.
In what follows, we understand “we” as our collective selves, the one that is numbered as “the population” and addressed to as “the masses".
As some German philosophers once noted, there is and has always been a struggle between the governing and the governed (in current phrasing, the citizens and their governments). Compared to feudal societies, modern societies give less power to the rulers by distributing powers along with counter-powers: violence and repression abilities are given to the police, but the police is made accountable for its deeds and must abide by rules written in law; policymaking is left to politicians, but politicians are sanctioned by elections on a regular basis; etc. Powers are made accountable to counter-powers.
Anonymity is unaccountability for the masses. It is therefore an ambivalent concept. Murderers stay unpunished until the police succeeds in identifying them, in which case we see anonymity as a bad thing: it favors a bad behavior. Meanwhile, citizens vote anonymously at elections, in which case we see anonymity as a good thing: it favor a good behavior, freedom of speech, by shielding individuals from self-censorship.
Fear of retaliation cements our societies. When you speak out your mind, you expose yourself to retribution. When an employee accuses his boss, he risks putting himself into conflict or being fired. Thus, he won't do it lightly. but when the gravity of the situation overcomes his anticipation of the harm that it will do to him. For more dramatic example, when Edward Snowden exposed the doings of the National Security Agency (NSA), an agency of one of the most powerful countries in the world, he changed the course of his whole life (fleeing to foreign countries, seeking political asylum, etc.) and brought upon him urgent threats (assassination) as well as long-term ones (extradition to his country for judgment and punishment). Still, his perception of how wrong the doings of the NSA were overcame his fear and he took upon himself to act. As it appears in both examples, fear of retribution filters bold actions: most people will never deviate from the collective behavior, but when this behavior becomes damaging or contradicts fundamental principles, some individuals may deviate and act in defiance of retribution.
In contrast to taking such stands, anonymity is a way to dodge retaliation. It lowers the barrier set up by fear of retribution, which is why, for instance, comments on public websites are sometimes noisy and filled with innate behavior; an old source of complaint on the Web. Yet, in spite of the burden of irritating behaviors, we argue that it is in our best interest to fight for the ability of anybody to act anonymously on the Internet.
Let us ask the following question: who retaliates? In a family, it will be one's relatives; in a company, one's peers or superiors; in a society, governments or powerful corporations; that is to say, the ruling class.
In the course of its surveillance program, the United States government has been targeting its own citizens. Among many examples, the XKEYSCORE program automatically flags for extra surveillance people reading a monthly technology magazine such as the Linux Journal. That is to say, a government developed technology by which behavior that was formerly anonymous and free of consequences, such as reading a magazine, becomes nominative and pushes targeted individuals one step further on the scale of potential retaliation. At first, this move was a victory for the American government in the struggle that opposes it to the American people: for ten years, it leveraged additional power and control over the population without counter-power nor accountability; that is to say, at no cost.
The question of anonymity on the Internet thus arises in the current context of nation-state mass surveillance. It is the new battleground in which the struggle between governing and governed continues. In this fight, the former are gaining ground by developing surveillance technology (PRISM, XKEYSCORE, ...), identifying you uniquely from the public information your computer sends when your browse the Web (see the Panopticlick), wiretapping undersea fiber optic cables or recording your online behavior. The latter are developing anonymization technology such as the Tor Project, increasingly using encryption to raise the cost of surveillance  and putting the fight to political institutions, as the Electronic Frontier Foundation does.
Looking at this fight, it is clear that anonymity is power for the people because it is one of the main things that government technology has taken from them. It is clear as well that encryption is power for the people, because governments are trying to take it away from them (for instance, attempts by governments to outlaw encryption that is too strong to be deciphered by state agents). Now, both anonymity and encryption can be used by criminals to exchange information out of the control of the state. As such, governments will argue that they should have the ability to overcome them in the name of prevention of crime. But it is nowhere in the interest of the people to let them do so. As Smári McCarthy points out , such arguments rely on the assumption that the government is just, that it will use this power for the public good. These arguments are grounded on trust. Yet, it should never be necessary to trust a government. Whenever trust seems to be needed, a counter-power ought to be created to establish, not trust, but accountability.
Counter-power do not appear by themselves. They are created when citizens gain the upper hand in their struggle with their government. This is the reason why we need to fight our best for the establishment of a right to use the Internet anonymously and a right to full encryption of our data.
 Smári McCarthy, Engineering Our Way Out of Fascism