I agree with many of your points in your post dffr1. I used to subscribe to Consumer Reports but gave up the subscription a long time ago. Yes, there was a time way back when they were on the Honda bandwagon and as you say rated them a best buy. Well, I decided to purchase on that analysis and ended up owning 5 straight new Honda's that included 1 Civic, 3 Accords, and 1 CRX. Never had a bad one and drove them all till they dropped. Well, then I went off and bought another vehicle that CR highly recommended and that was a new Volkswagon Fox. Worst car I ever owned, sold it pretty quick and lost a ton on it. I dropped my subscription to Consumer Reports and never picked one up again. So, the moral of the story is most buyers who have good experiences with ownership, will most times be inclined to continue until they have a poor experience with a brand. Word of mouth from other friends that own a vehicle play into it as well.
Now, lets get back to the Toyota problems! If I was driving a Toyota and ended up having an accident in it caused by a problem that had been acknowledged by a recall, I would bever buy form them again. Recalls are common in the auto industry and they are meant to protect the buyer. When they become repeated by the same manufacturer, then some may question reliability issues and go to another brand. Now, this bad publicity that Toyota has received pertaining to the recent recalls, it may hurt them in the short term, but the jury is out on the long term, some may decide like I did to try another brand, and then stick to it!
Consumer Reports is in the business to sell magazines! Sometimes they are correct, sometimes not! But Americans are sometimes lazy as I inferred earlier in this post, and tend to continue with brand until they have a bad experience.