See the media reports. Vinnik is accused of laundering $4 billion in cash through BTC-e. That amount is the entire trade volume of BTC-e. So the American authorities think that every single user (including me) of BTC-e engages in money laundering. We must act against this.
Even though it may seem so, I still haven't found any sort of article explicitly stating that it is in fact BTC-E that has been used for said accusations. I am however glad that the server(s) haven't (at least, it seems so) been compromised by the authorities. In terms of people's funds, if the authorities seized everything related to BTC-E, people will have a very hard time seeing even a penny back. Investigation alone could take years due to the size of this 'scandal', and another thing, if people will be offered an opportunity to withdraw their funds, they will likely have to fully verify themselves in order to get back what is theirs. That way the authorities can precisely see who and what sort of people are involved in using this exchange.
Edit; it seems that after reading the latest articles BTC-E does indeed get mentioned.
take a look at their tweeter account : 
