In a survey done on a load of microbically swabbed households, the loo was clean enough to eat from - and the most disgustingly dirty, dangerous and infected thing was the 'fridge door handle.
It's only really Legionairre's disease you need to worry about in fine water mists, and current troubles with allergies and infections is not enough exposure to bugs to build up immunity!
I've never had any illnesses from leaving the loo lid open when flushing, or given anybody food poisoning.
(I wasn't too sure about the loo in the campsite in Andorra, back in the '60s. It consisted of two plates for your feet, and a hole in the floor - and when you flushed it, your feet got "washed" if you were too slow to leap away. :wsh: )