Antibacterial soaps do kill off the beneficial bacteria on your skin that would normally help keep the bad bacteria in check. Washing your hands well with regular soap is just as good if not better, as it actually removes the bacteria from your skin. Those antibacterial gels that you leave on will kill most things, the alcohol denatures the bacterial cell walls and also kills viruses. Not every kind, but the majority of the kind you will run into on a daily basis. You also leave it on, allowing it to actually work.
Killing all the bacteria may eventually lead to resistant strains, much like we have found with antibiotic overuse. Those resistant strains are more virulent and then harder to kill when we really need to kill them, like when they are making us sick.