Call me a conspiracy theorist all you want but you can't just go there and build a system that is a potential threat to the USD world reserve currency and to the power of the FED.
I understand some Bitcoin fanatics of the cryptolibertarian and anarchist persuasion would like to believe that anything not a blockchain is a house of cards destined to tumble, but everything Ulbricht is charged with would still be a crime if the Silk Road ran entirely on dollars and cents, so to me, invoking conspiracy doesn't really pass the smell test.
If the government weas really that afraid of dark markets, or bitcoin, one would expect it to take heavier action against sites like Coinbase, or other open businesses which accept it, since they have far greater potential of spreading Bitcoin to the masses than inherently illegal sites like Silk Road, which would make most people uncomfortable even to know about. Yet, merely holding Bitcoins, or transacting in BTC, is not a crime.
Also, there's nothing stopping the US government from simply using BTC itself, or whatever cryptocurrency it sees fit, as it might any foreign currency.
I've never seen any sign that the Fed or the USG actually see cryptocurrencies as a threat.