It's at the bottom and maybe skipped by some people.
It seems to me anyway that most if not all mods so far have this flag set wrong. If set at all.The save="false" parameter (or save="0") will prevent your mod to be "recorded" in the savegame.
It should be used when your mod only changes graphical settings or game values, that have no lasting effect on the game. (like the player's run speed in stations...)
With save="false" the user can disable the mod (or delete the whole folder!) and the savegame will not be invalidated.
This seems to be why people have to go and manually delete a mod section from their save file when removing a mod.