Our saliva contains some compounds which act to inhibit the growth of these organisms. However, the presence of food particles in our mouths and growth adaptations by the bacteria allow the bacteria to flourish. Because of this it is necessary for us to brush our teeth . When we brush our teeth we do not kill all of the bacteria in our mouths, we do not even come close. By brushing our teeth we remove food particles and dental plaque from our teeth.
Dental plaque is formed when bacteria use our teeth as a place to grow.
So the toothbrush acts as a method to remove the dental plaque and therefore remove bacteria from your teeth. Some toothpaste brands have compounds like fluoride which act to kill bacteria. However, the toothpaste will never kill all the bacteria, therefore there will always be some survivors that will replenish the population. Ultimately we are trying to control bacterial growth by removing there source of food. For example food particles stuck in our teeth.