I had fun reading all the Rosarito Beach stuff, never did see the list of rental car places but haven't looked through everything yet.
I think I got the matter settled though and wanted to share for anyone that's interested. I made reservations through Advantage and called to double-check that we could take car to Ensenada and they said yes. My rate for four days is about $180, plus Mexico surcharge. This might sound steep, but the convenience will be worth it for us. We usually go to Southern Mexico, first time to Baja, so we really want to check out the area on our own.
Our hotel offered to set up transport from San Diego airport to hotel and back for $320. This isn't really bad, considering all that entails, but we wanted to have the car to roam and stop along the way.
I enjoyed reading about Puerto Nuevo in the Rosarita posts and really want to stop there, as well as Rosarita, on our way to Ensenada.
Thanks again for the comments and help.