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If you kill 99.99% not 99.9%, of the germs on your hands, the other 0.01% are not killed and they remain on your hands. The probability that you kill just as many bad germs as good germs is the same. Eventually, the germs, good and bad will start to (multiply) grow back and eventually reach the same concentration as before antiseptic use. This cycle can be repeated over and over. This is why you must kill the bad and good germs over and over. Hand antiseptics and sanitizers do not distinguish between good germs and bad germs. If your hands become contaminated by bad germs, you want to kill as many bad germs as possible as quickly as possible to keep you from becoming infected with a disease producing germ.
Your analogy with dogs is not applicable to this discussion. It is not possible for an antiseptic to distinguish between good germs and bad germs. Antiseptics kill all germs. Therefore, we cannot select for bad or good germs using an antiseptic or sanitizer.
We do not want to kill all germs with antiseptics nor can we kill all germs with antiseptics. There are many very good germs in and on our bodies as well as in our environment. An example of a good germ is yeast. Yeast ferment sugar to alcohol which we drink and also use in antiseptics to kill bad germs. The bottom line on antiseptic use is we want to keep our hands as free from germs as possible. If we reduce the numbers germs on our hands, then we reduce the chances that we will become infected with a disease producing germ. It is a numbers game.
Not all humans carry C. difficile in their digestive tract. C. difficile is found in some hospitals as endospores. Bacterial endospores are very resistant to many chemical disinfectants including antiseptics. Endospores are also very resistant to heat and drying. Therefore, endospores contaminate many hospital environments. They are also not easily grown or detected. Patients in the hospital for systemic infections are often treated very aggressively with oral antibiotics. Unfortunately, the oral antibiotics kill the good and bad germs in the digestive system. If and endospore of C. difficile is ingested and starts to grow, it can produce a toxin (poison) which kills the cells of the digestive tract causing a sometimes fatal disease called pseudomembraneous colitis. Pseudomembraneous colitis can be treated if the disease has not progressed to far. Your point is well taken. Perhaps oral antibiotics should be taken off the market and all serious systemic infections should be treated with intravenous antibiotics.
Good germs will not protect you from bad germs. Individuals who have never used antiseptics or sanitizers will still become infected with many different disease producing microorganisms. These microorganisms cause infectious disease like typhoid fever, gastrointestinal flu, the common cold, and H1N1 (swine) flu, just to name a few. If we reduce the number of germs, we are exposed to on our hands our chances of becoming infected are reduced. That is the purpose of hand antiseptics and santizers.