Earlier quoted context omitted.
But it works that way even if you book on the hotel's own website... Or Hotels.com, Booking, whatever you want.
Just because it's being done by different companies it doesn't make it right. It's a shady way to lure customers and mislead them. They manipulate these fees in order to have a lower price displayed on the search results.
If you hate Hotel Tonight because of the fees, you shouldn't be staying at the hotel actually charging the fees.