President William McKinley cited reconciliation between the North and South in a speech that followed the conclusion of the Spanish-American War on December 14, 1898. A number of former Confederate officers had volunteered for service during the war, which had helped secure U.S. victory, McKinley said:

… Every soldier’s grave made during our unfortunate Civil War is a tribute to American valor. And while, when those graves were made, we differed widely about the future of this government, those differences were long ago settled by the arbitrament of arms; and the time has now come, in the evolution of sentiment and feeling under the providence of God, when in the spirit of fraternity we should share with you in the care of the graves of the Confederate soldiers.

The Cordial feeling now happily existing between the North and South prompts this gracious act, and if it needed further justification, it is found in the gallant loyalty to the Union and the flag so conspicuously shown in the year just past by the sons and grandsons of these (Spanish-American War veterans).

What a glorious future awaits us if united, wisely, and bravely we face the new problems now pressing upon us, determined to solve them for right and humanity.

That flag has been planted in two hemispheres, and there it remains the symbol of liberty and law, of peace and progress. Who will withdraw from the people over whom it floats its protecting folds? Who will haul it down? Answer me, ye men of the South, who is there in Dixie who will haul it down?

McKinley called for Federal recognition of Union and Confederate soldiers because he viewed them all as Americans. But the Confederate flag wasn’t a part of McKinley’s reconciliation efforts, and he specifically cites the flying of the American flag in the South as reason to move forward with Federal recognition of Confederate soldiers. Unlike the McKinley era, however, some currently argue that the Confederate flag should be considered and offered protection because of its historic context.

You may also be interested in Confederate Flag Debate : A Little History Lesson

The Confederate flag didn’t fly widely in the South until the 1940s, the Atlantic reports:

After the surrender in 1865, Confederate flags were folded and put away. They were most likely to be spotted at memorials or cemeteries. Even after the hopeful decade of Reconstruction gave way to the violent repression of Redemption, open displays of the flag remained rare. There was no need for a banner to signal defiance; Jim Crow reigned unchallenged.

The flag slowly crept back into public life over the ensuing decades, saluted at veterans’ reunions, promoted by the United Daughters of the Confederacy, even carried into battle by units from the South. By the mid-twentieth century, the flags were also waved by football fans, and sold to tourists.

But as a political symbol, the flag was revived when northern Democrats began to press for an end to the South’s system of racial oppression. In 1948, the Dixiecrats revolted against President Harry Truman—who had desegregated the armed forces and supported anti-lynching bills. The movement began in Mississippi in February of 1948, with thousands of activists “shouting rebel yells and waving the Confederate flag,” as the Associated Press reported at the time. Some actually removed old, mothballed flags from the trunks where they had until then been gathering dust.

Whereas Confederate and Union soldiers are considered equal under Federal law, some critics argue that the same doesn't apply for the American and Confederate flags. It must be noted however, that Confederate monuments, statues and flags located in public areas are already protected by law. Some states have also recently enacted Heritage Protection Acts that give further protection, namely historic preservation, to their respective decades old Confederate memorials, obelisks and edifices. But unlike granite and marble monuments, flags do age and wear out and need to be replaced, so some argue that once the tattered flag is retired, its successor should be barred from entering the public ground. But on the other hand, others are quick to point out that any flagstaff could find itself protected under the current Heritage Protection Act.

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