Here is a link to a detailed article about how CR collects and analyzes their data on reliability. (I cannot tell easily if the article is available for non-members, because I am a member so I can see it, but it may not work for everyone, sorry.)
Consumer Reports' Car Reliability FAQ
CR makes it clear that reliability is based on reported "problems," with problems ranging in severity, not only on problems that cause a car to be out of service. I think most people would consider a car to be less reliable if it needs to go to be repaired frequently, not just that it won't run. Over the many years in which I drove Mercedes-Benz cars, which used to have a reputation for very high reliability, my cars left me by the side of the road and unable to drive only once or twice (leaving aside accidents and tire failures). But they sure spent plenty of time in the shop for fixing things and cost me a lot of money. My family's Hondas and Toyotas were much more reliable in the sense of needing fewer repairs and costing less money to repair, but they did occasionally fail to operate.
Here is a quotation from the CR article, explaining how CR says they assess the relative importance of various types of problems:
"Are All Problems Considered Equally Serious?
Engine major, engine cooling, transmission major, and drive system problems are more likely to take a car out of service and to be more expensive to repair than the other problem areas. Consequently, we weight these areas more heavily in our calculations of model year overall reliability verdict. Problems such as broken trim and in-car electronics have a much smaller weight. Problems in any area can be an expense and a bother, though, so we report them all in the reliability history charts."
One other point that might cause confusion -- CR presents reliability ratings of existing cars, with color-coded charts showing the data for each car make/model combination in 17 categories. So that is fairly straightforward. But they also do
predicted reliability on new models for which there is little or no data yet. I suspect that news stories about these ratings sometimes fail to distinguish between the two.
(And on another point of reliability versus consumer preference -- We also had a Jeep Grand Wagoneer along the way, and it probably ranked low in reliability -- the carburetor and ignition system were trouble spots as I recall -- but we loved it! It was a fantastic trailering vehicle.)