Re: The Paradox of Tolerance summarizes my opinion:
You hit the nail on the head with the Chomsky quote.
Bugger Popper's paradox. Even if he's right, he's wrong. If you decide you won't tolerate intolerance then you're intolerant. Simple as that. There are other ways of fighting intolerance than becoming intolerant yourself. They may ultimately (in the very long term) be ineffective, but in that case both options lead to the same end and the only question is do you get there by keeping your principles or abandoning them.
To the argument I'll throw in John Stuart Mill's On Liberty where he argues at great length that we should never censor minority views. Go read it.
I'll also throw in Voltaire's example. He wanted his enemies to publish their opinions so that he could destroy them using their own words and arguments.
I'll toss in a cliche too: "Sunlight is the best disinfectant."
Implicit in the freedoms enshrined in certain jurisdictions regarding speech, religion and political views is that you have the right to be wrong. Not to do wrong but to think wrong. You can think and say what the hell you like. There may be legal consequences if what you say is defamatory or if it incites criminal acts, but otherwise your speech should be legal (no matter how fucktarded it is).
Almost orthogonal to this is the first amendment to the US constitution. That applies only to the government. The government cannot apply prior restraint to speech (they can't prevent you saying anything). The government may deal with your speech post facto if, for example, it incites violence. The courts, so far, have mostly held that the first amendment prohibits the government from prosecuting you for saying something they don't like (mostly, because books saying that marijuana does no harm have been prosecuted in the past).
Individuals and corporations, in general, are not constrained by the first amendment. You can say what you want but you can't make a company rent you a megaphone to say it. Freedom of speech is not freedom to force others to hear it or to force others to sell/lease/give you the tools you need.
Different considerations would apply if the internet in the US had "common carrier" status. As I understand it, it doesn't. So registrars and hosting companies can discriminate against certain customers.
For those who think censoring nazis is a good thing, consider the current US gov't. It comprises people who like neonazis (or at least pretend to so that they can get votes from neonazi sympathisers). It comprises people who think abortion is always bad (even for incest or when both mother and baby will die if an abortion is not performed). It comprises people who think universal health care is bad (and are defunding advertising to get people to sign up for Obamacare). It comprises people who think global warming is a hoax. Do you want to set a precedent of censoring internet speech to these people?