There are no studies to back me up. Despite this, I'm convinced that the use of hand sanitizer in a non-institutional setting causes people to get sick more frequently. In institutional settings (i.e. hospitals or long term care facilities), studies have definitively shown that the use of hand sanitizer dramatically reduces the risk of spreading infections from patient to patient. However, to my knowledge, the use of hand sanitizer has never been studied in the general public. Just like we have different guidelines for treating community vs. hospital acquired pneumonia, I believe the use of hand sanitizer works differently in the community than in a hospital.
In hospitals, most of the patients are already immunocompromised. They're sick. They have open wounds, catheters, tubes, and other entry points into the body that aren't in your average person walking the streets. Hospital workers must frequently wash and/or sanitize their hands in order to prevent resistant bugs from being spread patient to patient.
In the community, people are relatively healthy. They generally aren't immunocompromised in the ways that hospital patients are. In addition, a healthy person is covered from head to toe in bacteria. Lots and lots of bacteria. However, this is not a bad thing. The normal flora covering your skin and mucosal linings help keep you healthy. The presence of this normal bacteria prevent more dangerous bacteria from adhering and forming growing colonies.
I postulate that hand sanitizer in a community setting is bad for you because it does exactly what it claims to do. It kills 99.9% of bacteria on contact. The only problem is that it doesn't discriminate between bad and good bacteria. It just kills 99.9% of everything on your skin. Therefore, upon eliminating the normal flora on your skin, bad bacteria are better able to latch on and replicate unimpeded.
People seem to have this idea that we should live in a sterile environment. They spend an inordinate amount of time cleaning and sanitizing themselves and every surface they might ever touch. It's next to impossible to convince these people that they actually have an immune system, and it does fight off germs if you let it. However, when you kill off your normal flora with sanitizers, you're weakening one of your body's primary defenses against infections.
I just wish someone would do a study on this. I'm almost positive that it would show people who use hand sanitizer regularly get sick more often than people who don't.