The Maquis used hit and run tactics, making swift, calculated strikes, getting in and out without taking too much damage, and they hid out in the Badlands, where the larger Cardassian vessels couldn't maneuver fast enough to avoid the plasma flares (see 'Caretaker' for an example).
And there probably was some concerns at Central Command that the Federation wouldn't take kindly to just wiping them off the face of the galaxy. After all, Cardassian 'justice' is well known, as opposed to the Federation's desire to rehabilitate any criminal element, and these were once Federation citizens. The Cardassian government would probably be worried that wiping out the Maquis would strain their relations, if not get the Federation lined up against them, supporting the Maquis.
And yes, the Jem'Hadar DID effectively wipe out the Maquis. Dukat practically says as much - he swears the Maquis would be wiped out in five days. At that point, the Cardassians weren't looking to keep the peace with the Federation - with their new Dominion allies, they could risk war without concern.