I suppose that it is part of the fabric of countries such as ours that such contradictions arise. We are a liberal democracy, which should not be confused with liberal vs. conservative viewpoints. Liberal democracies and liberalism itself has a deep respect for individual rights and a reluctance concerning governmental interference with those rights. As the late liberal political theorist, Richard E. Flathman, wrote in Reflections of a Would-Be Anarchist, liberalism is "committed to the ideal of individuality" and to the "widest possible freedom of individual action." One of the great virtues of our form of government is that we don't try to force viewpoints upon people but instead allow a wide breadth of viewpoints to be expressed. And, if people want to hold contradictory views, so be it.
Interestingly, liberal thinkers such as Flathman can at times sound somewhat like tea party members in seeing freedom as primary. Only warily and reluctantly does liberalism accept "the necessity of government, of law, and of a partly rule-governed politics that takes its focus from the existence of the established authority of government and law." Governmental interference is only reluctantly accepted when it is necessary to such things as safety and security. Of course, it is the nature of our times that we will have to consider just how much interference is warranted. Threats both foreign and domestic are very real. In this environment we must balance the contradictory elements found between security and freedom.
The desire to fly a Confederate flag will hopefully fade as its offensiveness to a large segment of our society is recognized. What should not fade, as any good proponent of liberalism will tell you, is the freedom to express viewpoints that may run counter to the majority and, yes, may not even make a great deal of sense.