Hand sanitizers claim to kill ~99% of bacteria. How does this work? Well, alcohol kills bacteria exponentially. For example, after x amount of time, 90% are dead. After 2x that time, 99%, 3x, 99.9%, and so on. As you can see from that math, you'll never 100% sterilize something using alcohol - at least not in a practical way. However, as far as getting germs off your hands, 99.9% is good enough. You're not looking to sterilize your hands (which is impossible), you're looking to cut down the risk of infection.
The 10% survivors in each instance aren't resistant, they're just lucky. Maybe they didn't get the full exposure to the alcohol, they had a little extra water in them, or they were in a clump. The effectiveness of a sanitizer is always dependent on the surface to which it is applied. If the alcohol can't get to the bacterium, it can't kill it. As such, human skin provides a lot of nooks and crannies in which bacteria could not be reached by the alcohol very well. This is why alcohol based hand rubs are only recommended on non-soiled hands. They aren't designed to penetrate dirt and gunk. Just like the ratio of bleach to water has to increase depending on the amount of blood (or protein) in a spill.
Also, while alcohol kills everything, it doesn't efficiently kill everything. Bacterial spores, bacteria with thick capsules, and nonenveloped viruses are fairly resistant to alcohol. For this reason, alcohol is never used as the only method when something needs to be completely sterile - we use fire, 10% bleach, formaldehyde, gamma rays, or autoclaving instead. Labs also use the aseptic technique when surfaces need to be 100% sterile. Please see the CDC take on handwashing and hand sanitizer.
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