In my home country you have the constitutional right to visit a judge at their home to plead particular kinds of cases.
All the same, threatening the judiciary is one of the most anti-social things you can do, and should be strictly policed. I don't know if trawling news comments is an effective way to do that, but I'm glad to know they're making an effort. A few false positives (appropriately handled) is a good sign of sufficiently high sensitivity.
It's great that we have these laws and the U.S Marshalls to enforce them since a lot of jerks wind up in civil litigation because civil litigation is how one can deal non-violently with jerks who try and screw with people's businesses, and cause damage and harm. These jerks are used to getting what they want through intimidation and well... being jerks. Without this kind of protection, there'd be nothing to stop these jerks from getting their way through continuing their pattern of intimidation.
In my home country (that I share with the US Marshalls) you have the constitutional right to express a desire for harm to come upon anyone or anything, regardless of whether it's a federal judge or not. It's worrying that a federal agency would do anything in regards to comments that are clearly protected by the constitution.
It's quite the other way around: threats must be very specific in order to not be protected speech in the United States. Saying 'let's burn this mother down' during a protest is protected speech, for instance. In general, the threat must be specific and imminent, such as 'let's go to that building right there and do $violence right now!'
They have been mentioned several times in this thread, but you should consult Popehat's writings for in depth breakdowns of what is and is not protected speech.
Pointing at a person during riots and screaming "Kill that muthafucka now" would almost certainly cross the threshold.
Organizing an unofficial Wannsee conference to plan a genocide of $UNDESIRED_GROUP into details would not, even though the entire event would be a hatefest.
All the same, threatening the judiciary is one of the most anti-social things you can do, and should be strictly policed. I don't know if trawling news comments is an effective way to do that, but I'm glad to know they're making an effort. A few false positives (appropriately handled) is a good sign of sufficiently high sensitivity.