My impression is that a big part of the outrage is directed not at the conviction, but at the disproportionate sentence.
I'm not surprised or upset at all that he went to prison, but unless I'm missing a ton of details (and I probably am), 12 years is plenty for what he did.
It's the scale of the crime (he facilitated 10s of thousands of transactions), the judge clearly stated she wanted to make an example of him and give pause to anyone thinking about doing something similar in the future, and she was angry at the many of the letters of support Ulbricht's fans family and friends sent the court.
My memory is she started the sentencing hearing by disdainfully reading a few of them from a pile of them she brought to the court that day.