Are you thinking of "Dragon Flyz"?
Here's an overview of the show:
The year is 4180 AD. Our planet, completely devastated by a great
natural cataclysm, is covered by dark swamps and shaken by violent
The last survivors of the human race have built a flying city,
Airlandis, and drift above the turmoil, in search of a region spared
by the destruction. But this will not be an easy quest...
Dread Wing, a tyrannical mutant warrior, has proclaimed himself sole
ruler of the dying planet, and that includes the human's flying city
too! For the four Dragon Flyz - Z'neth, Summit, Apex and Peak and
their flying mounts - the Dragons - a bitter fight begins against
A description of the "wings" that enable them to fly:
All the main characters, good or evil, ride dragon mounts into battle,
but have the ability to fly short distances themselves. The
Dragonators make use of a technology whereby dragonfly-like wings
(known as "Exo-wings") emerge from the back-plate of their armor;
whereas Dread Wing and his minions the Dramen literally 'sprout'
membraneous wings from their shoulders.
More about the chief bad guy:
Dread Wing is the chief antagonist of the story, established in a cave
complex known as "Warnado" but anxious to live in the sky. His Dragon,
Blackheart, is the only one seen capable of breathing fire.
And just for the heck of it, some trivia:
Dragon Flyz was based on the Galoob toy line of the same name, which
featured action figures that could actually launch into the air and
float down, helicopter-style (similar to the same company’s Sky
Dancers toys). Like most other toy-related cartoons, this show’s
fortunes rose and fell with its plastic counterpart. When sales of the
Dragon Flyz figures didn’t meet expectations, the animated series was
cancelled, leaving fans with only 26 episodes of memories.
~ Edited from Wikipedia, Dragon Flyz Wiki, TooNaRifiC and The BIG CARTOON Database