Useless tonneau cover!

I don't know. I now have an Extang Tri fold tonneau on a Ram. That leaks too. It's an acceptable amount though, only small amounts of water. Actually I never had a tonneau that didn't leak even a few drops. That comes with the territory when you get something that's removable and has no permanent sealant like a silicone bead. And you really can't use that on the trifolds that lift up off of the truck bed rails.
But, also in the past, I have used some household window type sealants that helped stop water coming in.

 

Edit, just realized the thread was dead a year ago. But maybe this info will help...

The thing to keep in mind is that Toyota's beds aren't waterproof, or even water resistant, until you put some effort into sealing them. No tonneau will seal a bed that already leaks.

Truck canopies are no different. Before I had mine installed I applied RV style sealant under the black plastic bed caps (between the caps and the metal underneath), and put RV putty in the huge gaps in the front of the bed. There are numerous threads on here with more details and instructions on doing this. I would consider doing that before abandoning your cover.