Here's just a short, non-exhaustive list, as to why rubbing your eyes is a bad idea:
* it's very easy to scratch your cornea
* touching your eyes or eyelids is an easy way to introduce infections
* rubbing can increase the pressure on your eyes, which can cause damage
* rubbing to try to get something out of your eye risks more damage, as now you're rubbing a foreign body around delicate corneas and such
Eyes are also special in that has a dampened immune response. Eyes are relatively fragile as a result.
There are times when you want to rub your eyes because they itch. Doing nothing is the best approach. Your eye will work it out, or the urge will go away. Same for when something trivial is in your eye. Your tears will flush it out.
For non trivial contamination, use water. I have to assume there are exceptions, but when in doubt, water will flush it out.