Rubbered Washer Nuts Direction?
Please post a picture of the item.



If you're talking about Nylock style nuts where the element is to prevent the nut from vibrating loose:



The metal thread goes on first.





If you're talking about a nut with a built in fluid seal, due to its design, a Seal Nut will need to go on with the rubber element on the inside.
The rubber must be compressed to seal against the surface it abuts, it's not going to seal if assembled with the rubber element on the outside.

 

How the seal works