Rubbing your eyes is a natural reaction, of course, we do it when our eye needs more blood flow or tears to the area for example when we're tired (rubbing brings more blood flow and therefore more oxygen and nutrients to the tired eye) or if there is something in our eye to help tackle a potential allergen or pathogen and flush it out. So of course, there are times when we need to rub our eyes! But rubbing can be hugely damaging - in the short term it could cause micro-scratches on your cornea (the front window of your eye). The cornea is an amazing piece of tissue, packed with stem cells so it regenerates very quickly if it is just a minor scratch (just like your tongue - you burn it one day and then have forgotten about that burn by the next day) but since we blink so much, if the wound is severe, it won't be able to heal quickly enough and then it can become a serious problem.
If you happen to rub your eyes when your hands are dirty you could certainly cause infection. A common scenario, is a patient who has been gardening or doing DIY work when something goes into their eye. The natural instinct is to rub it or to try get it out but with unclean hands, this can lead to other problems like infections.
In the long term, chronic rubbing (for example you often see this with children) has been linked to actually changing the shape of your cornea and causing an eye disease called keratoconus whereby the cornea changes from being a round shape to being a cone shape. This can be quite serious, affecting vision and often requiring special contact lenses or even surgery to stabilise.
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