CPU's are sequential processing devices. They break an algorithm up into a sequence of operations and execute them one at a time. on other hand FPGA's are parallel processing devices. An entire algorithm might be executed in a single tick of the clock, or, worst case, far fewer clock ticks than it takes a sequential processor.
One other key factor which makes FPGAs clock frequencies lower is the programmability of the connection within the FPGA. It creates additional signal delays. On CPUs the signal path is direct optimizes for speed.