There are masks and there are masks.
Within the ICU areas of the hospitals they fit masks for you that are tested to make sure you cannot smell or taste a noxious chemical. This is to make sure you dont manage to pick up the very bacteria laden air in the area.These masks should prevent you from breathing in the bacteria.
For normal situations (even on an aircraft) all you need is a basic mask to stop your coughs and sneezes travelling very far. Similarly, to stop you picking up things too easily. It wont prevent you breathing in the bacteria, but will make it less likely.