How often is FPGA used for UAV flight control?
A FPGA is a set of programmable logic gates made to excel in one thing, and one thing only.
A CPU is a set of fixed logic gates made to be used for a large variety of purposes.  

If you decide to use the FPGA for something, you better be using it often. Otherwise you're carrying idle logic. This is why a CPU is often more cost effective.
When you're not doing thing A, you can do thing B. With an FPGA the hardware for thing A is useless when doing thing B. But you can do them at the same time!

There are certainly use cases for FPGA on flight controllers. Performing checksums on the data interface, digital filters and signal processing. These are small tasks that can be outsourced to the FPGA, since they are expensive on the CPU.
Yet, flying is still a relatively slow process with little data, so CPU's can keep up. Compared to high speed video processing.

Also, development for an FPGA is more expensive. The parts are pricey, high pin count thus the boards are expensive (> 2 layers) and the design software is expensive. Overall, development costs more time, and time is money.