It is inevitable that while the USA transitions to the overtly suspicious mindset that has been the norm in Europe and the MidEast for some time, some mistakes born of good intentions are made. You guys are learning how to do this very rapidly; we've been doing it for many years and yet still misunderstandings happen. Take them as a natural consequence of the quite proper intent to protect your people; accept that over-zealous officials combined with enthusiastic amateur (and professional) pilots will occasionally result in a difference of opinion. It happens. Be patient, don't get too wound up about freedoms, and give every assistance you can to those who have the very difficult job of carrying out the new security regulations.
This is your new reality, I'm afraid.