Oh wow, yeah this is a problem we had as well. You need two things: A way for fresh air to come in from the outside to be burned, and a way for the exhaust to exit to the outside. This can be hard to accomplish, and presents challenges in cold weather with freezing pipes/etc.
If you only install a flue, you will burn cabin air and that air will go outside. What will replace that air? Anywhere air can get in, air will flow in. Now lets say you had a fan mounted in the ceiling pulling hot air out- air will try to enter anywhere it can get in, including through your flue. How does that affect functionality/performance/safety?
This is also a problem when for instance, you're cleaning your black tank. With the fan on, you pull the vapors straight from the tank into the cabin, and the tank vent becomes an inlet. Be conscious of positive/negative air pressure in the cabin and how all of your ventilation / heat sources / openings will interact.
Ultimately we went with a tankless water heater designed for permanent RV use as it addresses those issues. Its definitely not perfect, though.