NVIDIA GPUs are also innovative hardware, mentioned in the article, and CUDA is also just an extension of C. CUDA is wildly popular, and lots of higher level abstractions had been built on top of it. The only thing lower level than CUDA is the NVVM IR code which is generated by the C compiler (eg. LLVM NVVM backend) and is only compiled into final machine code by the GPU driver at run-time. So C is the lowest level.
The problem doesn't lie with the language, it lies with the x86 processors and different trade-offs that companies like Intel must make, such as trying to sell processors to developers who have been instructed by their employers to be productive and use a "safe" and high level language (e.g. Java CRUD application developers, or JavaScript web developers, etc).
edit: typos