Something you’ll note: all of these locations are islands. The U.S. Navy controlled the sea. Hence they couldn’t be attacked by large bodies of troops. Further, they lay at some distance from major Confederate troop concentrations and railroads (though, IIRC, Port Royal wasn’t too far off from a rail line). The Confederacy lacked effective naval forces barring a few commerce raiders and two half-functional ironclads (which were countered with rapidly-improving Union ironclads). And coaling stations were easily changed if it had become necessary - you just take over some other island and divert your shipments there instead.
So there wasn’t a whole the Confederacy could or even really wanted to do in order to deal with it. And as Sailboat explained, they couldn’t hold these areas. In fact, they had a very poor track record in coastal combat, because the Union Navy could and did choose any target it wanted at any time it cared for. In 1862 - the first real year of war - the Union effectively took control over the entire Eastern seaboard coastline. In1863 they controlled all of it and the Confederacy has no trade except in smuggled goods, basically. In1864 even that stopped.
Basically, the Confederacy had zero naval successes. They made a good showing for their materials and managed to permanently drive the merchant marine away from being U.S.-flagged. But in the end they didn’t accomplish very much in real terms. Not in the raiding, not in river defense, and not in blockade running. This is actually not really a huge problem in Civil War history, as the Confederacy was in a somewhat similar position as the American Revolution. Nobody sneers at John Paul Jones; he did many of the same things as Raphael Semmes. Neither couldn’t possibly match the high-seas Navy, so they didn’t. (Although I think Semmes was a madman for challenging the Kearsage, but he was a bit of a jerk anyway.)