I could be wrong, but I suspect the reason Londoners think that is just because they use it so regularly. If you're catching 2+ TFL tubes a day, and national services maybe a few times a year, maybe even a couple of times a week, if they both have pretty similar success rates then TFL will feel much worse, because it will get so many more bad memories.
I probably go to London at least ten times a month (either for a day or just for an evening), and have slightly more network rail trips a month (all my trips to london are an hour away by train), and in my experience I have much more trust for TFL.
This sort of perception is what makes one think that train services in other countries are always better than in your own backyard. The truth is that, in Europe, the average level of railway service is more or less the same everywhere these days; the exception is recent high-speed technology, which is only available in a handful of countries ( http://en.wikipedia.org/wiki/High-speed_rail_in_Europe ).
