A few points...
Consumer Reports is fine for what it does, but you have to understand how they get and report their ratings and look deeper. I wouldn't throw them away, nor would I trust them as my only source of research when buying a car.
Second, Honda is reliable overall, but it has never been more reliable overall than Toyota. Further, even a reliable manufacturer can make an unreliable model. And, even a good reliable car will have its weak points (the automatic transmission in many Hondas with V6s for instance, the stuck accelerator issue with many Toyotas, the airbag issue on both).
Rather than look at only a consolidated "score" for a vehicle, I would look at the details in the CR reliability survey data...
This was the first point I wanted to make. CR's overall rating looks at overall problems with engine issues, electrical system issues, and infotainment issues all going into the mix. I think they need to weigh them more giving major problems more weight than they do, since some make a car undriveable and some are only annoying. If you pay to subscribe (I do) you can look up how a car fares in each category, but if you don't subscribe you only get the overall rating with no way of knowing if it is based on major (and expensive) mechanical issues, or more minor (or cheaper) issues.
If you look at CR's breakdown on the Clarity, major mechanical systems that could lead to major driveablity issues, safety issues, or leave you stranded, are all rated much better than average. Engine, electrical, transmission, fuel system, exhaust, suspension, brakes, etc. are all rated as much better than average. The relative issues are: body integrity (average), paint/trim (average), power equipment (average), and body hardware (much worse than average). While these areas are annoying, and not something you expect from a well made car with a sticker north of $30K, they are not safety issues, or anything I'd consider a true reliability issue (they don't effect the car mechanically- it will start, it will run well, it won't die on you, and there are no safety issues).
Appreciate the feedback! Individual accolades about Honda aside, with which I would concur... , it wasn't a single report.
CR's ratings are, as I noted, “based upon thousands of owner reports over the past several years.”
This is semi-related to another area I was going to talk about. They quote you cite is their entire database. The ratings being "based upon thousands of owner reports..." is the database they use for every car they report on, not each car they report on. IOW, they may be using 5-20 thousand reports, but the Honda Civic may have a few hundred, the Toyota Corolla may have a thousand, the Chevy Silverado may have 3-400, the Ford Focus may have 100 or so, the Honda Clarity may have 50 or less. The more cars a manufacturer sells in a particular model, the more reports CR will have. The Clarity has not sold that many cars, so I doubt CR has more than a couple dozen (generously) on it.
So, now you have to consider the issue of sample size. If you have a sample of 100 reports and 10 cars had a particular issue, and another car with a sample of 1000 had 100 cars with that issue, you can be much more confident that the issue with the car with 1000 samples is more likely a problem with the car and not a statistical anomaly (caused by confounding variables). With the Clarity you may have 20 cars with 2 problems, in that case, with only a couple cars with problems, it still shows a 10% failure rate like the others, but the chances that the problem is just dumb luck and not an actual problem with the cars is now much higher.
The other issue is the fact that it is based upon owner reports. Now you are dealing with self-selection bias. People are more likely to respond if they feel strongly one way or the other. If they have a car that is a total lemon, they are likely to respond with all their issues. If they bought a car thinking it would be 100% reliable, but like any machine it has a few issues, and they are disappointed because they had unrealistic expectations, they are more likely to respond with all their issues. If they consider the car very reliable, they may either not respond, or they may unintentionally leave some issues they had out because they forgot them or just weren't thinking about them at the time. I know when I filled one out for my 1997 Sentra (I bought it new, it had a
ton of issues the entire time I owned it), I remembered every issue and looked for receipts because I was upset at having so many problems in a car that CR at the time said was very reliable. When I had my Hyundai Sonata (bought new in 2004) and my Ford Fusion (bought new in 2011), I thought of them as reliable, though they had some problems, and I wasn't as careful to look up each problem and went with my memory, and I probably left something out.
Now, all that said, there is no doubt that our cars have some problems. Looking at the forum, infotainment, Honda Link, and some intermittent charging issues are pretty common (and are all issues I've had as well). These are annoyance problems, not safety or true (IMO) reliability issues. Should we have them, of course not. Hopefully, Honda will resolve them. Should they keep someone from trusting the car, well, I guess that is an individual choice. If I knew about them in advance, I may have considered the Volt a bit more seriously, but I still probably would have ended up with the Clarity.