Eh, the evidence for it does seem pretty damning, even accounting for the fact that Ulbricht hasn't had the opportunity to defend himself (although, given the showing at the actual trial, perhaps he's better off). I would bet that he's guilty, though not even at 2:1 odds.
That's not to say that, strictly speaking, this isn't a miscarriage of justice - it is. No one should be in prison merely for selling drugs or facilitating the sale of drugs. But, Ross Ulbricht is likely a danger to society.