Several factors:
1) FPGAs are much slower due to the overhead of the flexibility they provide. With a lot of effort, you can get some FPGA designs (not even all of them!) to maybe 400 MHz on the more expensive FPGAs, and then it will do much less per cycle compared to an ASIC (CPUs are ASICs), so you need deep pipelines, with all the cost, complexity, and restrictions this entails.
2) CPUs have a lot of memory on-chip in the form of cache (several MiB), and they have sophisticated prefetch logic. In FPGAs, memory comes in several 100 blocks of, say, 4 kiB (depending on FPGA model). All memory management is purely manual.
3) CPUs tend to have a much higher external memory bandwidth.
4) Complex operations that are not directly provided by the FPGA fabric, like floating-point arithmetic or large memories with more than two ports, are expensive in terms of area and performance.
5) Modern desktop CPUs are incredibly well optimized: high clock frequency, out-of-order execution, superscalarity with several execution units, SIMD, automatic cache management, branch prediction, ... It's just very hard to beat that, and this is only possible for certain, very restricted applications. Highly parallel DSP (Digital Signal Processing) with integer/fixed-point arithmetic comes to mind.