Being barefoot inside is far worse than wearing shoes. Skin oils stick into the carpet and attract dust, fleas, and mites. Dirt and germs stick to sweaty skin far more than to the soles of shoes.
If you're going to take your shoes off indoors wear indoor-only slippers, flips-flops, or whatever. That's the cleanest. Otherwise it's more hygenic to wipe your feet when coming in and keeping your shoes ON!
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