Whether I agree with it or not, the law often recognises differences like this. It's not illegal to lie, but it is illegal to lie in the aid a murder. The lier themselves might not be a murderer, but the lier is knowingly facilitating murder.
Ulbricht was knowingly facilitating crime in the case, and sometimes this crime would result in the deaths of people. And despite knowing all this he took no action to address it.
Perhaps your point was he just didn't deserve the sentence he receive, which is fair, but he clearly did something that most people would consider very wrong.
I also wonder how people would feel if Silkroad was associated more with the trading of humans, CSAM, biological weapons or more serious things rather than just drugs. I doubt the "he's just running a marketplace" reasoning would hold in most people's eyes then.