I don't think that you are alone in this decision. All automakers have their ups and downs - but when a company like Toyota, known for superior quality control and build quality, is put under a microscope - little cracks are bound to be seen. You don't get to the top without making some concessions in the process - some corners will inevitably get cut along the way.
Honda has always been a top automaker, but they've also made some great improvements to the interior appointment of their cars. When I got my Camry (1996) - nothing that Honda offered was even remotely close to build quality, ride, and choice of material. Spring forward 5 years - not much as changed, as I was looking for a good commuter car - settled on a Corolla instead of a Honda. Now - Honda seems to have made a quantum leap in interior appointments and choice of materials. The Toyota equivalents seem bland and sparse in comparison - now, the only one that I would ever consider is the new Venza - not for build quality, but for its size and versatility.
I don't think that Toyota has dropped the ball on quality, if you sell more cars and trucks, there is a greater chance that something will be wrong - just a matter of statistics. Probably more accurate to say that the competition has been very aggressive and taking more notice of what people like to see in a car - quality control is much tighter and brand loyalty doesn't have the aura that it used to have. Toyota still makes a very good product, IMO, just that their quality "yardstick" of what is considered quality has moved down a couple of notches. I mean the Canadian plants still have one of the most streamlined manufacturing processes and top QC out there. I think where Toyota went wrong was trying to catch GM in the first place, sure it would look good on paper, but they forgot or ignored the importance of what got them there in the first place.
One point of the article was what I can "junk" journalism. Pretty misleading how the general media jumped on that tragic death of the family of four in the Lexus rental car. Toyota had to do a knee-jerk recall those floormats, when it appeared that the dealership "stacked" two mats ontop of each other, one being for a completely different vehicle. That is a recipe for disaster for any make - but for damage control, not sure if this had the result that Toyota is looking for. Plus, the 911 call showed that the family seemingly "gave" up. Of course we may never know what really went through their minds the few moments before the crash - but common sense would assume that a CHP trained office should be able to react to that situation by shutting down the car, pulling it in neutral, etc. etc. - but the fact is, doesn't matter what happened, people died and it was in a Toyota product, the public doesn't necessarily respond to logic or details.