So is the reason for this
(a) Some writer heard about TOR and wanted to use it in the show and didn't think of its positive uses
(b) The prelude to some move against the TOR network by the US government
(c) Someone trying to portray TOR as the ultimate way to conceal illegal activities, in hopes that gullible criminals etc. will start to use it and thus be open to scrutiny by e.g. the NSA.