It seems odd to me that questions like this on a technology site could somehow be used to incriminate people. Maybe the goal is to prevent people from asking questions.
What you ask can and will be used against you?
Let's use a real world example. The feds might present evidence in a murder trial that the defendant checked into a hotel next to where the murder was committed. Nobody would say that there is anything inherently incriminating about checking into a hotel, or that it's terrible that "checking into a hotel can be used against you." It's just circumstantial evidence putting the defendant near the scene of the crime, even though it is otherwise totally innocuous.
Similarly, nobody is saying there is anything incriminating about using Stack Overflow. But posts you make on Stack Overflow can be a piece of evidence in a chain linking you to a crime, just like a whole host of otherwise innocuous things can serve as that kind of evidence.
And making people feel that simply asking questions about Tor will put them in the same category as hardcore criminals is just wrong. We're not all heartless criminals. In fact, most just want a bit of privacy.
1) They were able to find code identical to the SO question within the SilkRoad source code
2) They already had circumstantial evidence linking him to the site, this just strengthened it
3) "frosty" is the user/computer name used to generate the private ssh key on SilkRoad's server, further linking him to the site
"although Tor has known legitimage uses.."