'Faster' is a relative term. It depends what you are trying to do.
If you have an application that requires lots of conditional logic (if-then-else) and general purpose computing with double-precision floating-point numbers, then its likely you can get your algorithms 'working' faster (i.e., elapsed time) using CPUs. Consider that the 'supercomputers' generally discussed are CPU or GPU based, and you can program using optimized libraries of code.
If you have a highly parallel system where lots of the same operations are required, and those operations are 'simple' eg., a multiply-accumulate (MAC), then using DSPs or CPUs or GPUs to implement a system can be less efficient than an FPGA. An FPGA allows you to implement only the logic needed for the application.
If a CPU or DSP can meet your requirements, and you know how to program it, then it is 'faster' to use that technology.
If the performance characteristics required by a system design are; implement the algorithm, take no more than XX Watts of power, and fit into YY space. Then you need to meet all the requirements, so what is 'faster' in this context.
Take for example the power trade-off. Comparing generic power parameters does not help, eg. which is better, a CPU with a maximum power dissipation of 10W or an FPGA with a maximum power dissipation of 20W? If your algorithm can be described as requiring 10 multiply-accumulates per 1GHz clock, then you need 10 GMAC/s of processing power. If the CPU runs at 1GHz and can perform 4 MACs per clock cycle, then its can process 4 GMAC/s, so you need 2.5 CPUs, i.e., 30Ws of CPUs. If your FPGA can process 4000 MACs at 500MHz, then it can process 2000 GMAC/s. The extra processing power of the FPGA can then be traded-off by running the FPGA at a lower clock-rate, or using a smaller device, or processing more data.
Signal processing systems are generally built using a combination of CPUs, DSP, and FPGAs. Using each type of logic where they perform 'optimally'.
Don't buy into marketing PR where a softcore CPU on an FPGA is the solution to all of your problems. It is the solution to some problems, but not necessarily the one you are currently faced with :)
Cheers,
Dave