I didn't see anything on methodology, but I'm assuming they're just surveying their users—in which case, I think it would make some sense for javascript to be overrepresented.
The TIOBE index has always been a bit weird. If you read their note about their methodology, you'll see that it's measuring something kind of interesting, but not really what you'd call "the most used languages." For example, IIRC part of a language's TIOBE ranking is how many college courses use it.
Do you know of another more objective source, though?
Other folks are citing Github and Stack Overflow, but they are just reporting on proportions used on their own sites, and I would not be at all surprised to find that both those sites are more popular with web developers than say Java or C/C++/C# or Visual Basic devs (all those languages outrank javascript on Tiobe).
That seems pretty likely to be true of Github. But for Stack Overflow, I would be really surprised. Stack Overflow has had a huge and thriving C# community from the start, and it's got so much page rank that questions about any language, "web" or not, are likely to lead there. The only languages that seem likely to be underrepresented are ones that are mainly used by people who learned them long ago and aren't gaining any more users (like MUMPS or something), since those people are unlikely to have questions.
