I recently did this and might have a little help. I had to keep both the polygon feature and the table it relates to in the document I published. Did you setup a relationship using relationship classes? Did you publish directly to ArcOnline or to your Server and than add it to ArcOnline?
I'm successfully viewing related attributes in ArcOnline from the spatial data to a related table. However if I have a spatial dataset related to a table which relates to another table ArcOnline is failing to pull the attributes from that 2nd table.