I think there are 2 big concerns:
- the level of humidity in the air (too much can create a nice place for bacteria to grow).
- the cleanliness of the humidifier tank (so bacteria can't grow).
We use a whole house humidifier which has a fresh water source (rather than a tank which can allow for bacterial growth) and we keep it at level that is considered "safe" when it comes to bacterial growth. We live in the midwest so it gets very dry, the humidifier has really helped with sinus trouble over the past 3 years.
Hope this helps!
ETA: Also, I don't hesitate to use the vaporizer (warm or cold, but cold is our favorite) in my cfer's room during a bad cold either bc it really seems to help. I just keep it very clean and don't run it for more than a few days at a time.