The phrase "flying black flags" refers to the black flags flown by jihadists. It's saying that after such a military campaign, those militants who had free reign to move around before are no longer able to move around freely, particularly not in groups or under their raised black banners.
Many are familiar with what some call “the black flags of jihad” flown
by Islamic extremists from Jabhat al-Nusra to Al Qaeda. The flags
vary in appearance, but most share a similar theme: they typically
have white writing on a black flag, and depict the shehada, or
profession of faith that there is no god but god, and Muhammad is his
messenger.
[Blaze.com]
ISIS Militants Are Now Flying Their Black Flags Over Iraq’s Largest
Oil Refinery.
[RYOT Headline]