fungus is not, I don't think, related to the case but to the general atmosphere in which the camera is stored -- cool and dry is best, warm and moist is worst. For long term storage take the batteries out, if any, and store in an air-tight case with something to absorb moisture -- one of those "do not swallow" dissicant thingies that come with most electronics these days, or even just a small cloth bag with some uncooked rice.
Carrying the camera in its leather case while using it certainly won't hurt it -- for that, bumps and scratches are the greater hazard, not fungus.