It's worth considering that if everyone is using super-hard encryption, IDing actual secret agents from hostile countries becomes orders of magnitude more difficult.
Also consider that developers and systems administrators (and in general the sorts of people who use ssh) are far more likely to have the technical know-how to launch a sophisticated attack.
Putting all that together, it would not surprise me if the use of ssh were used as an identifying marker by the United States government to single individuals out for increased surveillance. Grant you, if this happens I think it is absolute bullshit, but I think there is some paranoid bureaucratic logic that leads to this conclusion.