Yes, unfortunately too many people (particularly in the North) grew up associating the CSA battle flag with rebellion and not slavery for which the rebellion was fought. They also associate rebellion with patriotism (perhaps because the country began with a rebellion), so one gets the illogical position of attaching US patriotism to the very emblem that fought against the US.
This problem can partly--or quite plausibly
primarily--be attributed to the failure of Reconstruction and the view of the war that was allowed to predominate in the postbellum period; that of a war between brothers or states, or even of a "Civil War" of two factions equally loyal to the nation's founding principles (the CSA, after all, did put
George Washington on its seal) vying for supremacy, rather than a "War of Secession" (as it is known abroad), or even a "rebellion" (which what contemporary Unionists called it).
Lincoln's desire for a peace with "malice toward none and with charity for all" was noble enough, but the South--and many in the North--left Reconstruction with the view that the war was, as you said, a patriotic and justifiable act rather than one of treason. That is unsurprising- the penalties imposed upon those who engaged in treason and rebellion were woefully short of the level needed to ensure genuine compliance with the constitutional order and associated values, to say nothing of the usual penalties imposed on insurrectionists elsewhere. Their leaders never had to confess, much less face trial.
In short, Southerners were never made to think of themselves as the guilty party in the conflict, but instead that their "Lost Cause" had been a noble one, that the terms of Reconstruction were stringent rather than lenient, and that their worldview and idea of "American values" remained equally if not more valid as those of the Union. (And, in time, that their war, in fact, had
nothing to do with slavery at all!) Therefore, to them, their rebellion did not in any way represent a rejection of American values or patriotism, and so neither did its flag. This, of course, is wrong--but no one ever bothered to drive that point home.
To be fair, however, the justification of state authority against insurrection is always going to require a degree of cognitive dissonance in a country that is founded in the rejection of state authority by insurrection. Of course, one might avoid such problems by rejecting the initial insurrectionist rejection as illegitimate, but I am aware that shall always be very much a minority viewpoint.
she can call herself what she wants. I call her a vandal and a professional agitator.
The removal of a symbol of treason is a patriotic act that
strengthens the rule of law, rather than a contravention of it.