Before answering this, I did some research on it.
THE CASE FOR NO SHOES: It seems that every health expert says that wearing shoes in the house is a REALLY bad idea because of all the stuff that gets tracked in: e coli, bird droppings, bacteria that can kill a horse, apparently, and even carcinogens if you've been walking on an asphalt driveway, road, or walkway. The transfer rate from the bottom of the shoe to the carpet and flooring is over 90% most of the time, so figure it out.
THE CASE FOR SHOES: Shoes offer protection if you are prone to walking into the leg of a table or a chair, etc. Shoes offer protection if you have crumb crunchers around and they leave surprise Legos or other small toys for your feet to discover. If you keep your home's thermostat low to save energy, it's probable that the floors are the coldest area in your house, and wearing shoes keeps your feet from freezing off.
ALTERNATIVES: Have a "Mr. Rogers" pair of house shoes to wear around the house (but don't forget you're wearing them and go outside in them.) OR Frequently clean/disinfect your flooring by steam cleaning the carpeting and applying a disinfectant when cleaning the hardwood floors. OR Wash your shoes frequently in the washer to get them clean.
AS FOR ME... I have been wearing shoes inside for my entire life. I'm an old dog, but I can learn a few new tricks, I suppose. In the future, I think I'll wear slippers around the house (mine are a pair of moccasins so there is enough protection and warmth there). I will also resolve to pay more attention when I go into others' houses: if they have shoes piled up at the door, I'll take mine off. I want to be a good guest and will try not to walk around in a state of "arrogant ignorance."