Sometimes you just need a microcontroller to handle some tasks that would be immensely complicated to do yourself. Or maybe you want custom instructions that make use of extra logic on the fabric. I use a RISC-V in my design but most of the chip is dedicated as a modem, I just needed a way to easily send commands and receive telemetry without bit banging hundreds of pins. Another nice thing about using a CPU is that the logic blocks are reusable. I could write a bunch of verilog to receive data from an ADC once a second, average some samples, convert to units, and then send them out as ASCII but now those logic blocks are sitting idle 99.9% of the time. Instead I could have the CPU convert the data and then get back to work on other any other tasks using the same logic blocks. It's certainly possible to reduce area usage by trying to reuse blocks for other functions but it's a lot more work for the engineer.

You wouldn't have only a soft CPU on an FPGA, that's a waste of time and money.