It takes a great deal of care to get a C program correct and secure. That care means that you need to have really good people writing your programs. That means you pay more.
Also, C doesn't have the benefit of drawing from an enormous single standard library of functionality as .NET (and the other major web-centric platforms) has. So you may have to either buy components, or perform interop, or roll your own functionality which comes "for free" with a more, shall we say "web-centric" language like PHP or C# or Ruby or whatever. That means you pay more.
Add all of that to the fact that single-threaded computational speed just isn't that important on the web. If you need more scalability, most organizations can economically just throw more cores at the problem and be fine. This is not true for everyone, of course. I'd imagine that the core of Google's engine is written in C or a similar language not only for speed, but to save real money in power costs.