ATLAS is fast because its C code is generated beforehand by a more intelligent program. ATLAS is essentially the output of a compiler that has access to the information that would have been thrown away had your project been written directly in C. All the latest numeric libraries use this approach now, e.g. FFTW's backend is written in ML. The ATLAS overview paper (http://www.cs.utsa.edu/~whaley/papers/atlas_siam.pdf) explicitly states, "ATLAS does not require an
excellent compiler, since it uses code generation to perform many optimizations typically
done by compilers."
The point is that neither C nor the C compiler used to build ATLAS's output is what makes it fast. What makes it fast is essentially a different compiler which operates upstream of the C compiler.
Well ok, but someone sufficiently skilled could still hand-write code in C, using pthreads and SSE instructions, that will beat the fortran code every single time, because those constructs just aren't available in fortran and it's hard to claim that the compiler's always going to be better (as a Java guy most of the time, trust me, I'd love to believe it).
Why would pthreads and SSE instructions not be available in Fortran? Pthreads are just another library which Fortran programs can link to with no problem, and a modern Fortran compiler is perfectly capable of handling inline assembler.
Maybe it's wrong, I'm not knowledgeable about Fortran and certainly not horribly invested in this, go ahead and write a world-conquering BLAS library in Fortran if you want.
The text in your link claims: "it is illegal for a FORTRAN subroutine to call itself recursively, either directly or indirectly". That is not true anymore (for almost 20 years), since Fortran 90 has 'recursive' keyword with which you can declare that a subroutine can be used recursively.
(Also the all-caps spelling, FORTRAN, strongly hints that the link only talks about Fortran 77.)
FORTRAN's problems with rentrancy don't mean that FORTRAN programs can't be multi-threaded, it just means that each function has to be run from the same thread every time it's called.
I'm not saying FORTRAN is great - clearly it has a bunch of problems which C mostly doesn't have, which is why people mostly use C instead. But this one single advantage (allowing the compiler to do optimizations on array work) is so important to some people that it will always be around.
The point is that neither C nor the C compiler used to build ATLAS's output is what makes it fast. What makes it fast is essentially a different compiler which operates upstream of the C compiler.