I don't agree with the sentence either, but what he did, was not just "running an illegal website".
What else was it? It was just a market.... a free market at the end of the day. Most libertarians believe people should be able to take whatever drugs they wanted and this facilitated that for them. Obviously what he did was a crime in the eyes of the law but others would argue it was just a free market and people sold and bought what they wished.
He earned commission from all sales incl hard drugs, which is the definition of drug dealing and not just "running an illegal website". Also he didn't pay tax (of course) and was defending his drug empire with violence (Maryland indiction). He was conspiring with other people to maintain his business. This is not the same as for example release a free warez site or hacking stuff, which I would call "an illegal website", but not SilkRoad. Ross intended to gain money in form of Bitcoins with Heroin sales for example.
Drug dealing is drug dealing. He didn't directly sell the drugs but facilitated their sale only. And some people think taxation is theft but if govs legalized drugs then they could collect their taxes and end the drug war over night. He also hasn't been tried for the murder for hire and the case seems to have been dropped. Could have been entirely fabricated by the corrupt officers for all we know. Finally, warez sites usually make money from ads and commission from filehosters so they're still taking their cut
It doesn't matter how much you try to twist reality. Earning money with drug sales still make you a drug dealer. Conspiring with others in drug dealing makes it even worse.