My cats come in through the kitchen window, and step on to a towel placed on the work top especially for that purpose. If they are in during the day when I am at work, I have no idea where their dainty little paws might have been. 
Having said that, I don't prepare any food directly on the worktop, instead I have a variety of boards that are used for different things, i.e. veg, chicken, other meat etc.
Even so, I spray with Flash with Fairy and wipe down all the worktop every day, at least once and more often if Mr P has been cooking (he tends to splash when he stirs)
I think I operate a hygienic kitchen, no one has fallen ill to date.