Yes, fossil fuels are the best to keep pollution away, just need to installed perfectly, configured and maintained regularly, monitored to make sure everything is running correctly, and have additional properties lying around vacant just in case there are leaks, misconfigurations, poor installation, etc. But we must use fossil fuels, there are no other options!
I had a gas furnace that wasn't properly maintained as far as cleaning. Result: insufficient air flow for full combustion. Secondary result: CO build up in basement space. Tertiary result: asthma-like symptoms for me.
If this is happening, then you shouldn't be using that furnace/room!
Something beyond the furnace is not configured right.