I am in a similar boat-- fairly bad animal allergies and hay fever as a child accompanied with frequent and vigorous eye rubbing and now keratoconus (though, fortunately, not so far-progressed as to need corneal transplants).

My daughter has the same characteristic long eyelashes that I do, and exhibits allergies (though much less severe than mine). My wife and I have made a very strong effort to prevent her from eye-rubbing. She's old enough now to understand why we were so adamant about it.

I'm seeing elsewhere in this thread that nocturnal eye rubbing can be a problem. I never thought about that and it's a bit disturbing. I do remember waking-up with my eyes plastered shut with hardened mucus as a child.