Sleeping in a prone position is not bad. However there are some complications of it that can be negative. A simple example is drooling. A more important problem with sleeping in a prone position is poor posture. Most people don't have a bed like a chiropractic table that allows them to breathe with their face straight down while maintaining a neutral spine. Due to this lack of beds designed for the prone sleeper they have to turn their head to the side. This extreme rotation held for 8 hours can cause neck pain. Most people who sleep that way also use a pillow under their head and/or upper body causing excessive and prolonged lumbar extension. This can lead to low back pain. J Amer Chiropr Assoc 2011 May-June;48(4):17-18
The textbooks and the research I've seen always say the best sleep position maintains a neutral spine. That means on your back with a pillow supporting your neck and one supporting your knees. Alternatively you can sleep on your side with a pillow supporting your neck, head, and the top arm as well as a pillow between the knees. This will keep the spine in a neutral position. I always tell my patients that the best way to sleep is the one that gives you a good, full nights sleep. You can probably improve your sleep with a few modifications, but if you are a side sleeper, you'll have a difficult time trying to force yourself to your back because, you're not conscious at the time. The Mayo Clinic has some excellent images that can help with modifications.
People tend to sleep in positions that are comfortable for them. If all day long they sit or work in a flexed posture then their body may crave the extension of their low back that comes from prone positions. In fact they may sleep prone because of back pain caused by excessive flexion. We've all seen this phenomenon before as we squirm in our chair or our legs ache to stretch when on a long flight or car ride. Motion and proper posture affects every aspect of our life. More research can be found here (No Affiliation).