Marking his territory???

Okay, its good that you know not to rub his nose in it.  There is no way he will connect his mom rubbing his nose in the carpet full of pee, to "do not pee here" it has no connection for him at all.  So, it doesn't help and may make things worse. I've read that dogs with their noses rubbed in poop may start eating their poop.  but anyway, glad you aren't doing that anymore.  
If you did not catch him in the act, there is nothing you can do but clean it up with a pet cleaner that will break down the smells.  Since it is a valuable rug, I would remove it until the problem is resolved. If you still want a rug there, just buy a cheap one for now.  Do you have carpet or hardwood under the rug?  Be sure to spray down the coffee table with the pet cleaner as well.
If you do catch him in the act (not even a second afterwards will work) clap your hands or make a loud noise to distract him (hopefully stop him mid stream, ha) and then take him outside.