More than 300 flights, a fifth of the scheduled departures and arrivals, were canceled at Charlotte Douglas International Airport, an American Airlines hub. Dozens of other flights were canceled in other airports, including Raleigh-Durham International Airport, as well as those in Charleston, South Carolina; Savannah, Georgia, and Atlanta, according to flight-tracking site FlightAware.com.

Airlines canceled hundreds of flights to and from the Carolinas and Georgia on Thursday as Tropical Storm Michael pounded the region with heavy rain and strong winds.

The storm was weaker Thursday than when it made landfall in the Florida Panhandle Wednesday packing 140 mph winds, but the severe weather continued to snarl travel as it headed northeast.

Delta Air Lines CEO Ed Bastian told CNBC the carrier had scrubbed about 100 flights scheduled for Wednesday and Thursday due to the storm, which did not directly hit its hub at Hartsfield-Jackson International in Atlanta, the world's busiest airport.

Many of the airports affected by the storm are relatively small compared with those hit by other recent hurricanes, particularly the trio of deadly storms that struck airlines' hub cities last year, prompting the cancellation of more than 25,000 flights.

United Airlines, Delta Air Lines and American Airlines scrapped date-change and cancellation fees for several airports affected by the storm.