I wasn't able to build FRED using cygwin without changing the compiler for the following lines in FRED/src/Makefile:
lines 105, 108, 110, 172, 173, and 176
I just needed to change -std=c++11 to -std:gnu++11 and I was then able to make without errors, so I am guessing some of the dependencies are GNU C/C++ exclusive libraries.
Also, FRED/bin/fred_rt is hitting errors when I try to run it as-is.