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If you use something that kills 99.9% of germs on your skin or any other surface, what exactly do you think happens to the 0.01% that's left? They reproduce to fill the space left by the other dead germs. Also, they feed on the dead germs so they grow even faster. Now when you consider that the 0.01% not killed by your antimicrobial soap or hand sanitizer is the one that has already mutated to be antibiotic resistant, it doesn't take long to figure out that the surface will soon by populated by this type of micro-organism. Are you sure this is the surface you think is safe for your kids to eat on, or in the instance of shopping carts and babies, are you sure you want your baby teething on this surface?

My analogy is one that will probably irritate animal lovers, but here it is. We all know that dogs can be very dangerous when they attack humans. Suppose we decided that we would kill all the dogs we could find in order to protect ourselves. Suppose that our method of doing this only managed to kill breeds of dogs that are generally less aggressive, and the ones who are more aggressive survived and multiplied to fill the ecological niche filled by dogs. Soon all the dogs on the planet would be more dangerous to humans than ever.

If these solutions killed 100% of germs, it wouldn't be such a big issue. But they don't. We have no way to eradicate micro-organisms on this planet, so we'd darn well better not encourage it's population to be ones we can't kill when an infection with them occurs.

Also, regarding the question about C. difficile, this is an organism we all have in our digestive tract and it usually only causes problems when a person takes a broad-spectrum antibiotic in order to kill some nasty infection they have. C. difficile is resistant to these antibiotics so it grows out of control and makes people very sick. So your answer about good germs not protecting us from bad germs is also patently false.