The Bitcoin is having a small identity crisis at the moment. On one hand the whole idea behind the cryptocurrency is the anonymity that it provides, but on the other hand it is also trying to go mainstream and becoming a new payment method for the world.
While it seems like an impossible task to have the best of both worlds, having the FBI involved in the Bitcoin doesn't help in any way at all. The FBI is currently probing several of the biggest online Bitcoin exchange sites, trying to find proof of them having sold Bitcoin to fund drug trading on SilkRoad, a place where users could buy and sell all the drugs and substances you can imagine completely anonymous.
The FBI is looking into if the Bitcoin exchange sites provided Bitcoins to the owners and users of SilkRoad in exchange for fiat money, having issued subpoenas to exchange sites like Mt Gox. While the investigation has just opened, it seems that they might find what they are looking for, which might provide issues towards the Bitcoin going mainstream.
Making the Bitcoin become mainstream among regular people can become a lot more difficult than it already is, should the FBI find proof of exchanges selling Bitcoins to crooks to buy and sell drugs. A story like that will not be well received in the public and might hurt the public image that they have of it.