Confederate flag in retreat or temporarily in hiding, now would be a fitting time for Congress to right an egregious, 150 year-old wrong. That's where the American Flag Protection Act (AFPA) of 2015 comes in. AFPA would ban federal, state and local governments, as well as any organization receiving federal funds, from flying a Confederate banner from any building, site or facility.

Whereas the Confederate battle flag and all other flags of the government and states of the Confederate States of America from their inception have represented slavery, racial superiority, segregation, insurrection and treason;
Whereas the display of those flags therefore by definition is not a misappropriation of their meaning but using them as always intended;
Whereas more Americans died at the hands of those flying those banners than from all other wars of the United States combined;
The government of the United States is prohibited from displaying any Confederate flag or flag containing design elements from any Confederate flag at or over any building, facility, national park, cemetery, educational institution, military base or any other vehicle or site (museum and library exhibitions excepted).
No state or local receiving funding of any kind from the federal government of the United States may display any Confederate flag or flag containing design elements from any Confederate flag at or over any building, facility, park, cemetery, educational institution or any other vehicle or site (museum and library exhibitions excepted).
No company, organization or individual receiving funding of any kind from the federal government of the United States may display any Confederate flag or flag containing design elements from any Confederate flag at or over any building, facility, cemetery, educational institution or any other vehicle or site (museum and library exhibitions excepted).

There's no reason why the American Flag Protection Act of 2015 shouldn't enjoy the backing of a huge bipartisan majority in Congress. After all, in 2005 Sens. Hillary Clinton (D-NY) and Robert Bennett(R-UT) proposed legislation banning desecration of the American flag. In June 2005, the House easily passed a Constitutional amendment prohibiting desecration of Old Glory; the next year, the bill sponsored by then Senate majority leader Bill Frist (R-TN) failed by a single vote. And nothing desecrates or dishonors the American flag more than the display of the Confederate flag over any site anywhere in the United States or its territories. Simply put, "To ask Americans to walk beneath its shadow is a humiliation of irreducible proportions. And we all know it."
Just as important, AFPA does not prevent any American from carrying or displaying any Confederate banner on or within their person or private property. (For that act, there is no federal penalty, but only the opprobrium so richly deserved from true American patriots.) Under AFPA's "Posthumous Amnesty" provisions, all Confederate soldiers are pardoned for their treason against the United States, an act of compassionate forgiveness to be marked by the display of the Star-Spangled Banner alone over their graves. And for those who still sing from the states' rights hymnal, the American Flag Protection Act operates no differently than the expansion of Medicaid under Obamacare. States can always show their CSA flags with pride by choosing to opt-out of federal funding.