The cilia, as you probably know, are small projections off the lining of your lungs, nose, and throat. They work by waving in a coordinated fashion, moving mucus and any trapped particles up and out of the airways. In this way, they are an important part of your body's natural defenses against contaminants in the air and the environment.
Smoking cigarettes can definitely impair the function of your cilia. The smoke and the toxins it contains have actually been shown to 'paralyze' the cilia and keep them from functioning properly. There are many other effects on your airways from smoking, including increased inflammation and thickened mucus. All together, these harmful effects of smoking can predispose you to frequent colds and lung infections and also give you a chronic cough.
I highly recommend that you go to see your primary care doctor
about this issue. They can evaluate your persistent respiratory issues and help figure out what is going on and whether or not you need treatment. Also, I highly recommend that you talk to your doctor about the potential for help quitting smoking, which would be a very important step to take to improve your overall health.