Some of the things you expect to be clean get a far worser cleanliness regimen than some of the things you expect to be dirty.
Toilets are probably cleaned more often than restaurant pepper/salt shakers. Therefore one can expect the latter to be dirtier than the former.
Same with keyboards and telephones.
It depends on how you define "clean." Toilet water still have chemicals and deposits in them, including the agents from cleaning solutions.
Salt and pepper shakers basically have your obligatory bacteria on them.
Remote controls in hotels are extremely high in bacteria counts.
Eeeeeewww!