I have cats and they do get up on the counter. I shoo them off but, frankly, I'm not phobic about germs so I don't let it get to me too much.
If I'm making food for people other than my daughter and me, I am a lot more aware paranoid about cleaning and keeping everything off the counter and making sure there is no contamination.
If it's just for me, eh. I put bread on the counter to make a sandwich. I put spoons, knives and folks on the counter before using them. I'll put some crackers on the island/counter to munch on while I read the paper.
Germs are everywhere, even when you clean. They can barely be managed and never defeated. Our bodies are bacteria machines and transports. Thank goodness for white blood cells and antibodies!