The Founding Fathers, as well as the Confederate States, did not violate Romans 13 because they had Governments they followed (in both cases Colonial or State governments declared their Independence from the Royal or Federal Government).
We, on the other hand, are left with State Governments that will never stand up to whatever Federal abuses come their way, so we must 'grimace and bare it'. On the other hand, our Government is defined in the U.S. Constitution, and if said Government egregiously attacks this Constitution (e.g., voids the Second Amendment), the requirement to 'grimace and bare it' is not so clear.