Although the details of the gov's investigation and harassment of Jake are largely shrouded in secrecy, his harassment at the border began right after giving a keynote at HOPE 2010 in place of Julian Assange, as the only US citizen identified in the media as a member of the Wikileaks team.
Although I think what the US government has done to Jake is quite clearly a disgusting abuse of power, let us not kid ourselves by somehow believing that the state has gone after him because he has publicly advocated for the use of strong crypto.