If you google a picture of the 1907 Corn Palace you will see the Nazi Swashtika prominently displaced in that years decoration. History will tell you that before the nazi use of the symbol it had Native American importance as a symbol for good luck.
personally when I see a "don't tread on me" flag I think of the tea party and militias, I could live with the tea party reference but not the militia reference. I would not fly it anymore than I would fly a flag with a Native American symbol for good luck. Symbols get hijacked by organizations ... it happens.
I am sure that 90 percent who see it just think you are a member of the Tea Party.