Are there thousands of species dying off due to a chitrid fungus? I tend to be very skeptical of this (for instance, how does one even track the number of frogs there are in something like a rain forest).
There is a good wikipedia article on this subject, which has a lot of references that seem to be of high quality. You can also go to amphibiaweb.org or the national biological information infrastructure.
The "killer fungus" is not the only cause these sources mention. Other causes include habitat modification and fragmentation, pollution and climatic change.
It's certainly possible to count numbers of amphibians and it is not necessary to count them all to know that there is a dramatic decline in their numbers. If a sufficiently large number of populations around the world is counted accurately over a long enough period, and those populations are seen to decrease in numbers all over the world, I would say it is safe to speak of a global decline in amphibian populations.
Concerning the causes and what we can know about them: we can study the data, e.g. look at whether there are differences in decline rates between different types of populations (cool or warm climate, human density, food sources, amount of pollution), and we can study the effects something like the fungus has on individual amphibians, or on populations.
It's fairly easy to find a lot of information on this topic, from pretty reliable sources. I don't think skepticism is warranted here.