It could be that... it could also be kennel cough perhaps, which is basically a doggie version of the human cold.
You could put a humidifier safely next to his crate and under a "cave" of blankets at night if he sleeps in a crate. Our vet even mentioned adding vicks liquid to the humidifier water. That might help ease his nighttime coughing or breathing issues. And/or take him into the bathroom with you when you take a nice steamy hot shower, morning or night.
Otherwise you should probably just keep in good touch with your vet, and follow his instructions. If it is kennel cough, it can turn into pneumonia just like regular colds can in humans, so keep an eye on things if anything changes, and like I said, stay in touch with your vet. Don't worry too much, IMO, just keep an eye on things.
Lauren & Nikko