Try to look at it as zero something meaning that there is no problem with it.
Crime for instance isn't a problem when @ zero though crimes are still being committed. Individuals still have problems when loved ones are murdered, white collar crimes can still ruin someone, conmen still ply their trade. In short criminals still exist but not in a scale that Civ considers a problem.
Diseases still exist @ zero but not in any large scales. People still die of it but not in numbers affecting the gameplay any.
And so on.
A negative value of something a more positive value.
Negative crime means people go out of their way to follow the laws and rules, neighbourhood watches exist and report any people committing crimes, and so on.
Negative disease infers that people live healthier in a healthy environment, eating better, exercising better, avoiding health pitfalls, and so on.
Think outside the box. *smile* In this case think like the creators of the crime and disease and pollution system.
Cheers