Elligator is appropriate for use as a component in a steganography system, but in most cases the problem it solves isn't the hardest part of the system.
It's also useful in cases where you need to hash to a curve in a way that provably (in the ROM) doesn't have problematic structure. This comes up fairly often: OPRF, Boneh-Boyen short sigs, password-auth key exchanges like SPEKE and PAK, etc. It also was useful in SIKE, before that was broken.